[English] 日本語
Yorodumi
- PDB-6qlv: Crystal structure of W200H UbiX in complex with a geranyl-FMN N5 ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6qlv
TitleCrystal structure of W200H UbiX in complex with a geranyl-FMN N5 adduct
ComponentsFlavin prenyltransferase UbiX
KeywordsTRANSFERASE / UbiX Prenyltransferase Flavin binding
Function / homology
Function and homology information


flavin prenyltransferase / flavin prenyltransferase activity / lyase activity
Similarity search - Function
Flavin prenyltransferase UbiX-like / Flavin prenyltransferase-like / Flavoprotein / Flavin prenyltransferase-like / Flavoprotein / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / FLAVIN MONONUCLEOTIDE / Chem-HJN / Chem-HZZ / PHOSPHATE ION / Flavin prenyltransferase UbiX
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.391 Å
AuthorsMarshall, S.A. / Leys, D.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/K017802/1 United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/P000622/1 United Kingdom
CitationJournal: Nat Commun / Year: 2019
Title: The UbiX flavin prenyltransferase reaction mechanism resembles class I terpene cyclase chemistry.
Authors: Marshall, S.A. / Payne, K.A.P. / Fisher, K. / White, M.D. / Ni Cheallaigh, A. / Balaikaite, A. / Rigby, S.E.J. / Leys, D.
History
DepositionFeb 1, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 5, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Aug 21, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Flavin prenyltransferase UbiX
B: Flavin prenyltransferase UbiX
C: Flavin prenyltransferase UbiX
D: Flavin prenyltransferase UbiX
E: Flavin prenyltransferase UbiX
F: Flavin prenyltransferase UbiX
G: Flavin prenyltransferase UbiX
H: Flavin prenyltransferase UbiX
I: Flavin prenyltransferase UbiX
J: Flavin prenyltransferase UbiX
K: Flavin prenyltransferase UbiX
L: Flavin prenyltransferase UbiX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)305,83750
Polymers296,97912
Non-polymers8,85838
Water15,835879
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area54620 Å2
ΔGint-363 kcal/mol
Surface area65130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)161.533, 164.931, 102.527
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

-
Components

-
Protein , 1 types, 12 molecules ABCDEFGHIJKL

#1: Protein
Flavin prenyltransferase UbiX


Mass: 24748.256 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Gene: ubiX, C0044_29760, C8257_05245, CAZ10_26235, CGU42_07325, DT376_15100, DZ940_19110, DZ962_23875, NCTC13719_00955, PAERUG_E15_London_28_01_14_05236, PAMH19_1010, RW109_RW109_01660
Production host: Escherichia coli (E. coli) / References: UniProt: A0A072ZCW8, flavin prenyltransferase

-
Non-polymers , 7 types, 917 molecules

#2: Chemical
ChemComp-HZZ / [(2~{Z})-3,7-dimethylocta-2,6-dienyl] dihydrogen phosphate / [(2Z)-3,7-dimethylocta-2,6-dienyl] dihydrogen phosphate / (Z)-3,7-Dimethylocta-2,6-dien-1-yl dihydrogen phosphate / Geranyl monophosphate


Mass: 234.229 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
Formula: C10H19O4P
#3: Chemical
ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
Formula: C17H21N4O9P
#4: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Formula: C2H3O2
#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Formula: Na
#6: Chemical ChemComp-HJN / [(2~{R},3~{S},4~{S})-5-[5-[(2~{Z})-3,7-dimethylocta-2,6-dienyl]-7,8-dimethyl-2,4-bis(oxidanylidene)-1~{H}-benzo[g]pteridin-10-yl]-2,3,4-tris(oxidanyl)pentyl] dihydrogen phosphate


Mass: 594.594 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C27H39N4O9P
#7: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 879 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.75 Å3/Da / Density % sol: 55.33 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: PGA screen (Molecular Dimensions) C3 0.1 M ammonium sulphate, 0.3 M sodium formate, 0.1 M sodium acetate, pH 5.0, 3 % (w/v) gamma polyglutamic acid (Na+ form, LM), 20% MPD

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 3, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.391→115.4 Å / Num. obs: 108714 / % possible obs: 99.98 % / Redundancy: 2 % / Biso Wilson estimate: 26.01 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.08033 / Net I/σ(I): 7.02
Reflection shellResolution: 2.391→2.476 Å

-
Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZAF
Resolution: 2.391→115.4 Å / SU ML: 0.2569 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.8533
RfactorNum. reflection% reflection
Rfree0.2202 2016 1.85 %
Rwork0.1779 --
obs0.1786 108693 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 33.54 Å2
Refinement stepCycle: LAST / Resolution: 2.391→115.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17232 0 587 879 18698
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.001818243
X-RAY DIFFRACTIONf_angle_d0.47124964
X-RAY DIFFRACTIONf_chiral_restr0.03892893
X-RAY DIFFRACTIONf_plane_restr0.00443254
X-RAY DIFFRACTIONf_dihedral_angle_d3.066515153
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.39-2.450.29371460.25097541X-RAY DIFFRACTION99.99
2.45-2.520.27471410.22867500X-RAY DIFFRACTION99.96
2.52-2.590.26471400.22557529X-RAY DIFFRACTION99.99
2.59-2.670.25891460.21637528X-RAY DIFFRACTION99.97
2.67-2.770.25981420.20777591X-RAY DIFFRACTION99.97
2.77-2.880.30311370.20897545X-RAY DIFFRACTION99.97
2.88-3.010.24731440.20077569X-RAY DIFFRACTION100
3.01-3.170.24781450.19487588X-RAY DIFFRACTION99.99
3.17-3.370.24821440.18417600X-RAY DIFFRACTION100
3.37-3.630.20681440.16837611X-RAY DIFFRACTION99.97
3.63-40.18091450.15237630X-RAY DIFFRACTION99.97
4-4.570.18251400.13477685X-RAY DIFFRACTION100
4.57-5.760.17441490.1477748X-RAY DIFFRACTION99.97
5.76-115.540.19111530.16318012X-RAY DIFFRACTION99.93
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
14.49438604102-0.4633722544960.007603106304116.304592109973.264769949088.671234020160.188853264794-0.1220177279760.07815094244370.4103412059910.585366906505-0.11588831605-0.112177349540.209138109584-0.659148050760.168745080777-0.0234139077660.01960302097870.1600403939730.08560758569910.277247841579-29.881720116977.0444662687-29.8105796496
28.03246160967.419429969246.38937286686.830349195595.860101295975.9852183426-0.3518601136220.2589761572230.549957823194-0.3940386426230.1988543788730.706619484625-0.734348144652-0.3943653187370.5192006827350.197157002641-0.0180022827732-0.08071742098540.221702993510.08584374780070.359701070443-36.185463786582.7716083559-33.481301712
36.49947949514-4.08485721971-5.120899981967.552917976696.483646900437.20137789760.184679651315-0.3800997206910.4450411612950.2067120846130.295445075456-0.427659911078-0.0683537491053-0.360664770644-0.3669729502920.287720003856-0.00345662914462-0.1221526607730.2998006584370.02685254278570.229658186292-27.419753949182.0506038451-29.5854977398
45.365166884062.13623394291-1.028304765024.582152638562.506213727815.48574958311-0.3966084110610.0131301485479-0.328469791344-0.5570504589460.252110438410.291434562805-0.309701280976-0.08581082469190.139730496640.276411666837-0.102351121285-0.02821855838930.3366318657370.03106031556770.172319162208-29.746847904979.4930876789-46.450074963
51.336647998110.397083911865-1.210064887452.058333419282.355540173246.51104624137-0.16817364584-0.04850068726850.383549988342-0.3194980459860.155944817582-0.396847917767-0.3271021219250.3135705599990.08838729968190.265184699852-0.065945392898-0.03285653738780.2588393344750.07571438248460.346394852123-25.015080746388.5536990754-35.5522002226
62.05030619256-0.8435644401991.295540056847.91613570221-3.438917714982.382522400210.0262602407969-0.1683826879110.2724576631720.165325918585-0.375420023283-0.812979436771-0.13959219480.09098364048450.1854265706410.19781061339-0.0490215430608-0.03078121343330.3898063616310.02539382860180.343549368425-16.803771109374.9573535141-29.3261424612
70.780407164157-0.6213602077020.8956917533631.520743908080.1715513772351.69698249853-0.07213485387730.08824983406450.0486501441349-0.09216751279570.0377979623379-0.2796330725620.0399538970950.1905435437840.00608166051660.146948889064-0.01543861866790.01180087364850.2882074783340.03628717228770.260579305023-24.749978877366.5236374331-32.3985692642
80.334864838785-0.184029044734-0.09518432847842.583695306350.8318781432732.43574605477-0.0798206396423-0.00942043622573-0.117202442105-0.09121943380240.177854977817-0.110716786737-0.2647310537980.311769920406-0.1608114513390.1057364778770.01226462176070.005160212286590.2819072244280.05416496049910.16382150673-33.344174142465.6637332022-31.2222123543
91.457624691070.7005887600351.811461406630.6685884745182.143966861667.30589721122-0.111676854719-0.130929413488-0.0214478060270.117553572405-0.0478815625384-0.1576825566060.307740737822-0.0922137596180.00539572545780.126049857054-0.003598587594420.01923841772840.2884504010040.04930819923220.249487380125-33.863069155756.6969581955-31.8286196655
101.084383085630.3686521259270.7570349215741.82778283207-1.495350267684.60854753169-0.04298793891870.3096718925490.399535172129-0.0460990054069-0.02921684458830.211219171085-0.289923349373-0.3131880037920.1031964483350.158748018394-0.0267565704902-0.04347206623320.18919240305-0.003718901196160.292222895489-46.361915730671.9220356445-31.3835669198
117.53752683275-0.7684659830644.923180721072.589730446050.4526815681134.55385742864-0.116253691651-0.82533228570.442429224205-0.00774363880290.04659649736120.663886038691-0.341586803129-0.8935618333740.08382964933440.1979932619260.04850307605050.007471970142890.2107751692030.0001364098553760.326699375205-42.487473755378.1905653886-28.8447896119
121.956043147692.63819960075-2.151877031235.52287092019-1.826612141977.055918135540.08206772579030.180037814906-0.314791287479-0.415272280655-0.0455672685535-0.5918305039440.02701645622170.7044453218260.1069761793980.1979366411710.0933855289142-0.06444556115750.3658279247940.002514470463380.410484533839-2.4149201820927.2518565492-13.0031741153
133.228653846520.140719622843-0.3521072958030.7773107574310.2226981398261.319057802880.2383920115080.00872428970287-0.8149014259030.3824280647880.139895807128-0.1774872135910.523529223980.346092684322-0.0115256754261-0.2908856388570.128033933994-0.3444848096980.394393813273-0.02668993320690.516426946898-2.2051982868618.3954577052-10.0249028178
146.607801955560.410713516329-1.313944001252.53043162746-1.562250127814.93007633181-0.049768293989-0.209263965788-0.09310294310940.2025304363950.135388952541-0.1493371278840.00815507029972-0.0219830517542-0.01727092244250.1740018055530.0670474940863-0.08881591231270.331261022765-0.03415605029560.269292028573-3.9543419786824.2305708087-2.10313880736
154.41178298995-2.036906295181.162073314692.34955710459-0.8304546203971.08472009327-0.151976462665-0.1637191042840.01722372977450.2619132426850.0512619835224-0.400617782001-0.1390354224390.0761450206580.07929577846280.1955579779040.0331270873088-0.07973155367710.332405195474-0.01655936316590.3210162620370.76623817905930.8345116889-5.63840944113
161.701217877030.227773176498-0.7613167158692.905007621660.1800703038651.27814168183-0.01936271318410.03122718412990.1461985860340.2166448980270.186917365876-0.15613945525-0.0625202427477-0.054702232016-0.1379658127220.1339065879270.0288932363772-0.05966796609090.2918807734240.03280956094690.238932435353-13.478416559634.498206939-12.2614940171
174.305874288672.97881470647-4.089489173292.51451686152-2.017428915515.27463686506-0.0712716232654-0.002385860439930.307123313708-0.08888391134750.03336837363140.00866329030478-0.0786135759668-0.0438290084767-0.05795666683730.1233612774190.0407312702277-0.02803925023310.2548536497750.02750714296940.245256272645-22.419781504133.0746182465-17.6095615366
181.461612848231.371376831270.1203809690521.34674012572-0.3483377703113.063874851480.2879760429420.277468630259-0.5585797298880.229322924631-0.314458246337-0.7379173048290.7371548515880.0661445832213-0.05332591196630.00936556752540.105875235202-0.07894366650640.3957782044560.04447164291540.541783862634-13.869395591513.7367517621-18.5220177207
195.110131417515.07168430291-2.701773944575.35359274871-3.719741457585.37999042961-0.04532402601430.370884543954-0.655958674427-0.127479941711-0.0227187575085-0.5567078784960.26804236390.1901696549390.195579964350.2405607427160.105808879392-0.04682035142870.4037724734-0.06637503933060.448728281612-5.5786826820216.0445048868-17.9499120213
203.788437174441.44941246869-0.7173666166456.54172601033-1.01054956544.069216806460.0072996299072-0.3713397415840.352585745361-0.515217615741-0.140355272875-0.075359145058-0.4041006669960.374063146223-0.04618598463790.115679381841-0.01906124966470.06044713901750.368670008081-0.08898116907580.256060119631-49.641670881864.9250385444-5.59644181868
214.80752237091-1.314159106190.403784838647.89230505168-0.8342189582491.17566996652-0.140547248631-0.8442901292680.4138537951660.5347123305450.1683872955230.136849103414-0.01755984251990.309743107086-0.03738771675110.1807149235560.07065562694690.03795881725920.420665080956-0.06439272609380.326509359054-51.456159543264.14957316073.58127292894
223.437039956590.964933122845-2.246316629096.07761505421-1.149997272532.562472264410.0752694390013-0.3453321122810.1607408731090.257217286625-0.1124518296450.0491104129453-0.144861560572-0.01728074743960.04505387980620.128770968388-0.02674123878640.01776352040040.310031947018-0.05191865047420.257827176776-59.084647418562.1177856189-2.28948744925
236.18454815822.128721592424.418915337196.109019797940.2290752251266.58064078840.0529262430991-0.3332899055080.888501275760.653211651741-0.2810429648670.54496982134-0.427169066335-0.2299326421610.1387689285570.2144769452460.01396679242510.1105664174080.341331221699-0.07460716240550.41192312061-63.012266321169.3254814097-0.385913085939
240.653186839546-0.079625881755-0.235854313930.8322019861810.2324770931531.135407500560.04967781874090.08941394567640.143814748634-0.0220215926242-0.05679385139390.157561326526-0.126878166497-0.110295001025-0.002877882905850.135581422509-0.003885678822120.004234570635480.316865280312-0.02190344439490.264502141066-50.784940413461.5409797042-13.0725902165
257.367822740436.00607965157-2.029721893989.45467891553-5.279054521663.508201467050.2442496797330.266155082257-0.146121487681-0.239245350071-0.199605831018-0.3661802746250.2930470560890.5602823912060.02491456060050.1374019692990.0223367254911-0.005575137334050.350151929996-0.04176342792650.154134033757-41.238397055647.822976853-14.2759083926
264.877084767471.31271903739-4.215853135842.38224729446-1.760224306655.81845986289-0.00578689501144-0.5232814125720.2673550707680.434838529560.1745542655240.1743336372-0.150394556241-0.334929196226-0.2120304322160.149809074850.0646973217752-0.02607990560410.297167639807-0.03035129499630.26133991688-40.526613347653.88482211294.45344285889
275.432419319662.82830868681-2.150410334463.157165552040.3230669268993.093838645840.19465743224-0.5709275607760.2914559087950.681349526928-0.250160264117-0.295555732337-0.7790980465980.663712579570.142105884990.247843409866-0.0136734922953-7.94518464443E-50.449627748091-0.06992634957620.30306977807-43.06201362261.333486154.7601345646
285.913742599160.322980012338-0.1924714734763.43080327126-1.460728521942.756926994570.027933231272-0.655578695512-0.3287244696860.239948066364-0.0723628908965-0.1655217383890.324977316339-0.0673892453386-0.09823203725940.19501381389-0.01196364966940.03347492490380.277806320342-0.01940964584350.331807548565-62.182634244327.9560118871-14.3433709051
292.28357895014-0.37578410914-0.7227550990912.3503190644-2.981458536375.23992841326-0.01803063443330.0359659876234-0.2685761196-0.1557049879590.3061575577390.4009291399990.614300180456-0.0431508038789-0.2231642680820.135413299951-0.0696723184030.05108219470280.402577551756-0.07847736197380.355903288729-68.0804436623.4340320017-20.0787058901
303.83387144996-0.1917575555030.5021775103762.28123163259-2.635157568835.78531840308-0.01727945437250.2329231683960.0788620165885-0.06869792693730.02556044048280.2144409113760.141264471673-0.55705566071-0.04664873928010.147131087192-0.00972425888930.02265542784360.271416177405-0.03002808636440.368647726513-71.089999295232.9786218422-19.5216773277
317.13906310832-0.3963417468130.7803454096254.14935147281-2.888121021243.83211810223-0.220797891567-0.185062944640.3913077750310.1312375232340.3571872351860.09747159550540.228859755108-0.827997478236-0.02135268837050.167035398178-0.03773101546050.06512344643530.411874523819-0.008310829790740.363143151256-77.12256626630.782899194-13.6330261771
323.158958209241.28012462555-0.5299362680591.649708286930.6500057767021.252469115890.0325472214708-0.5138760573580.1979760707770.241419629702-0.1589086324930.1780732083470.04919714093280.06024146765170.06176865967490.155243308121-0.01021928885430.05524070516010.2804041628150.004298261229220.310313357139-64.156783260334.8414101854-10.0564056081
330.28164297178-0.157517204522-0.6012647547951.207962403950.4193050826782.21822505027-0.00363029544476-0.05333962185570.07195105722020.0878857207315-0.1315831175990.152648782792-0.0556659942767-0.07094003872640.1274241606680.0936231988357-0.005199334686150.01544168958010.26425833322-0.01159067599960.281371117409-54.473767629837.6556352767-18.7455258459
345.22618275243-3.189817358914.770362317963.32419567646-2.455991824065.102388123020.1552107497050.029849558967-0.312131918099-0.144123407758-0.202698328384-0.06448233027010.1236571139410.6015485879570.04884396236080.136080681027-0.01792205246190.06631937539750.25198219104-0.02984353710120.215224161286-46.435856612636.9974405705-25.4792102273
353.98528813682-1.228801969830.9168025366640.455723972132-0.6003762943331.829690688740.116034748967-0.0770477695937-0.3527148595320.029522919292-0.3416690456520.4538619863610.267692232324-0.2990686907490.2433704100180.131650947824-0.0194388468130.05537717763340.2803553473710.01838716677870.27738194141-57.445169754119.6459657511-30.2635033552
365.2541341881.508641733144.782591889683.330827158782.296967887984.897179452920.1513752195340.163165281302-0.7756627198580.2013075673960.05152751245690.03815217287880.92355832307-0.234811818706-0.2538349672980.199997977902-0.01785819866980.02878744016330.3002022174880.005140957474080.402269431333-60.617497094718.6134164678-22.7982537574
375.44780568192-1.43805569105-0.5559680018095.808493591630.4436541062053.7917615067-0.151390909949-0.2719321571440.359981055350.2208802600410.1304670356930.150915933268-0.323430731227-0.154516284258-0.0471971389110.1787158545390.0162225001662-0.09952656433040.3185577275940.00519296375810.334886270339-16.361801149363.2623496074-2.23603110852
388.21061098088-5.72544661414-3.987700274454.420437461661.268133760257.44013807808-0.351045961268-0.1737737176330.3663128774910.1730640677810.349789609676-0.433483586679-0.6348780948350.8118339314210.014674468530.214518564862-0.0688426534953-0.09618162639780.449020607846-0.05764345777980.394435624884-8.0548274033167.4787194844-2.98325123425
394.80959055503-3.084809177560.7700379155514.80661336722-3.044299507835.2279450540.0751806126116-0.03892395068790.2281864801210.461720602336-0.1831666559410.0719634431453-0.6569754885770.08948530000820.1192267772210.178495534312-0.0293927106342-0.03878157998510.301463356426-0.08774804275820.327925664942-15.711069329565.86939958812.65959844104
403.85229479116-0.822986969814-1.051234820822.421441246642.175173729243.465654063350.0266814951217-0.167272561960.07465939492120.07607835859920.0591735900342-0.2070218327630.11555382860.392115124816-0.03471557663330.1795315030650.0417212531976-0.09180128420250.329889692199-0.02107155648160.309881564125-2.8068479312955.08744088492.97804258237
413.15149292058-2.001404773781.519866533882.38890637021-0.04202999580334.56600557184-0.111104270247-0.8098407912470.6951732709720.1747459584920.288043620592-0.478854638764-0.5107784468860.215121036190.07014237965820.1805210586180.019708591317-0.1457960062310.559687840354-0.1715665434610.382975136447-7.5889414161264.30172135439.9267781087
421.474755673630.9598181481870.9360192506022.065796855771.087958260981.864393203160.0161919822584-0.3442458323250.1068680744720.2532737548240.01640469741750.02741177092480.0799772136423-0.160535968471-0.03000051744380.1628967723650.0279931882894-0.02565400071450.400884710948-0.0166688032170.22604585662-20.945832054555.99174155660.986246411838
432.80420031533-1.18731822648-1.353499266183.073170848341.626759049881.15604803109-0.246192831818-0.136652081470.001887432023230.2671321793010.161651333875-0.05517789686430.201282712733-0.0958328210740.01910873536340.1468875419860.0123310687045-0.05953819655240.3515303513940.03442290219440.222775711631-17.834709917855.8086140538-11.5696414067
446.83446612449-6.6967811458-1.055745662296.771339764340.6982227083651.743215685720.2296298442660.345619428058-0.148855582897-0.0592610044779-0.3345426140830.3031232498510.0921932587233-0.1575350761890.1017831602750.117349959989-0.0535355633514-0.0393651473140.319241499138-0.01597344226530.226339405844-20.573015390849.3983529929-17.2824609587
456.361782759910.380679834932-1.665349711442.677101530290.03145266868813.098936508540.1240249273450.1150500728840.537292988148-0.130046629520.0190759528732-0.276304046393-0.5632531640750.134371775555-0.136108267070.222106846206-0.0156816181917-0.04563013483820.242859928247-0.0005276302767250.303098150253-9.7406417228167.5519089346-14.545853912
469.169373418681.3356414388-4.732091145486.8220062709-0.4249648607854.42501634832-0.27997454665-0.188058653387-0.3885582316310.4093602255570.1812788380450.237793476390.478673033853-0.07157207655960.09284701398920.2683701022520.0362880768187-0.04736982516990.2778528987790.0602007310620.250825338191-35.81614493398.82420655775-17.502268128
472.80829053299-0.0822266247668-1.242444055482.875256710880.8829469065344.67636549906-0.00672108164836-0.159887538301-0.6096209009270.09209043648860.0530677265027-0.1000326154870.4468085497420.0232160398119-0.02187560481710.2110280029680.00935534350484-0.06675717761330.2555896512660.04794986394060.506704338683-30.97006525460.42956351998-20.0738723089
481.196184228180.1431653397170.5310227990594.11968736068-1.043568532051.838406331920.0421732947431-0.163080008353-0.351108829591-0.235084679886-0.01212809911710.1839202837540.23667131797-0.206560890081-0.0603769547370.160989534812-0.00864596961862-0.02100230910570.25996876494-0.005731383165180.327499861957-39.270590962611.3841126638-25.469761236
492.865208576330.2487711917841.279580571541.420680754580.06388919059272.032085502530.0350164663502-0.211995970774-0.2030518958750.1247737783330.04637795899620.08298263430820.0143446857573-0.0790374950665-0.06600134665330.1293809053020.00199593954619-0.005152963822150.233279602743-0.003827634629050.223221055638-26.893012676820.1340447588-16.4412778984
504.75755458851-3.278351532221.953365770453.99243868168-0.8473605310294.53636193770.125559512137-1.25218358789-0.8873585158450.6225540396270.2333279489470.1192923544020.149690901732-0.010121261163-0.1840209532170.268609024608-0.0205491630347-0.04131823432220.3567473578090.1121354572110.325428874475-28.38680430899.39468805207-6.93356262867
512.230075787020.5727581458760.5133538395554.27074513186-1.151724969574.16063071980.06112063642190.0974798088927-0.0588361605972-0.143189675809-0.1246501645180.314805084461-0.0407111472697-0.08378323500890.02454758556670.1184618424650.00679553758263-0.02323830205330.273274769964-0.0941062306020.265109453442-52.205798569519.270495358-49.6734225459
526.79383008984-4.624573306530.195280377748.39761988912-3.272823279648.39155655118-0.03309343050210.4068450224330.178030017309-0.70587192040.1050053557470.3292774984520.933980849503-0.787169601834-0.1157833697120.252534641866-0.0331656880139-0.081971254490.370199694413-0.1509131103780.332944820089-52.377226601412.2406513909-56.9956649913
533.43417155591.358674741320.08624077224042.006904079841.597735658682.65190237682-0.02392852835870.310200322098-0.0705086093676-0.2602307033260.235737424939-0.11779328471-0.01067405786780.291543758332-0.2040932681340.17394673250.0200595793803-0.009054801111290.289522478619-0.03159484705210.234619715147-42.830684269122.5362989656-54.161756394
541.07006165596-0.358861160849-0.1671515426320.418911981164-0.04138387429941.73099915083-0.01254175663470.201326245764-0.0567305454094-0.03314619672670.0789881596702-0.02380724129920.07863887775990.0811445779024-0.06435805840690.1185382442030.00194966019243-0.02187090650280.276073576563-0.04907902795310.259723956624-40.639757956927.2116511215-41.9282538284
550.9205767544022.07246745285-1.698769562364.64898450017-4.033046017224.78586726885-0.0612287943002-0.03613988008820.107377802683-0.187566616640.002800575361170.1331718082970.03410953613790.5029811667760.2093988273920.1194116257050.0201855901735-0.003690236154260.286398790123-0.006770958861690.211674955026-41.745913441332.195216265-32.5264152178
562.737238541480.84674558729-0.798186281013.75702035551-1.254385780082.73920270931-0.174738490390.285892922389-0.00404513676588-0.06091495763340.02602183374960.5263101485840.0726534958179-0.5766952393190.1165690273230.149129715502-0.0207914275709-0.0276146535010.326748485269-0.07192628628120.254213287025-60.375778598630.3592286914-37.7915876166
575.790022121684.48552029105-3.963539439765.9351658369-1.961602784033.1471668518-0.006778872916590.3912632207310.205967029458-0.5155827885920.1294915496580.782331521665-0.0648970343466-0.829332420295-0.1157098891050.1941533098610.0162694993728-0.1063045362980.408190790045-0.03351276547240.351569619553-61.107022435529.247786681-46.1009799166
584.8515527986-0.2890912035550.8351280286483.475683959460.04778924690265.120286846090.03604462837210.4552982431570.416204802013-0.4100792104620.09956257097440.08612700626310.0213643434285-0.202569078867-0.03497830653940.147497861856-0.0280871964545-0.1090635186110.2908118576570.0601547358020.353708089604-58.995252021561.0096481325-44.1590411333
593.20126043209-0.4636109941150.3997492861863.700111647332.914671650834.88590093078-0.1070052610590.0281488069950.390242806318-0.310093518724-0.01685858017050.405258117304-0.23521285315-0.2308695945510.163506689580.2025238134760.0326738532582-0.1142429538230.3033562593180.0331115796410.371502010211-64.87037640563.3133498877-37.7398647815
604.55019978258-1.27864064295-1.361934520881.897075839580.2576806543853.05803228706-0.2468477032740.0991052069764-0.390347820769-0.367805101977-0.4191813952410.702755006647-0.294753239312-0.250151461939-0.03927675607080.3103701193820.0829236751996-0.2632015719770.372959883901-0.0100833806020.561919028839-71.948961096563.4388641856-42.1644840052
611.90138867087-0.3139387228520.4593244696721.6438049047-0.7546964134041.01147263934-0.04209496750640.0396274062915-0.1389059612-0.1792864474740.03783519365740.3737620465550.079084086173-0.0580947859828-0.03336544086150.1379290101290.00981919644302-0.05677522702170.337557032022-0.02234538282990.335305418381-60.61166323750.3891071627-36.523451257
620.2383870274870.310992387953-0.1052143869232.982995170651.254883392942.080344626130.02041696553170.05365036292990.0586784792293-0.0774704911902-0.1342948401760.14510201925-0.0189060187468-0.124341861090.1199497194680.111927743327-0.00409349366681-0.02678353988520.2493675353930.05576955597730.29129656405-48.831197281855.6948695431-36.0603420722
631.348184066262.064320237410.7233111091388.887078545076.43769722285.463443335280.1855791609280.0824943750091-0.1823492506380.376885609075-0.0728002148562-0.4187657620070.399798362869-2.21753715433E-5-0.1537167427140.1267971424830.02511788915950.002193106399360.2620202493320.07190919461740.239525503961-42.409084891453.0450749089-30.3074109661
643.45766528982-1.415751038130.02285846076926.862279622810.8857089218680.275827577153-0.01071826803540.439677720310.42453574173-0.4515304217940.1090672065370.647619093805-0.1242133379110.0280007580799-0.04716652810490.154486692058-0.0343735873557-0.06606813776430.3404576358990.01649770608880.182091251247-44.721379661267.200096208-43.8356036997
652.3877408521.868555552390.9272797761063.548605078923.57439706254.31347089976-0.002566999403580.1276053314050.19674662926-0.965193713863-0.083943773304-0.105546614728-0.4035730042680.1932521164370.1615884610490.294650034973-0.00761929831026-0.08906943242810.3707857934790.06302366836960.246145356651-50.849169963665.2453464181-48.2884620198
662.176095227680.401228480693-0.4120229597635.62762656445-0.3256190510413.48751343896-0.0458127654223-0.48380501525-0.2402308845260.575144321951-0.002056315669080.1480720176250.259118002542-0.1363383615860.04470983488890.3050433828540.04406631299620.04527882462340.5038569862690.08273696727380.189932000761-35.743025697433.440425712414.5587439533
671.70061595275-1.14882701663-0.002248710826261.44635840873-0.02207712036080.849629368002-0.0697062469191-0.251000514296-0.1157392245840.1995291157230.06027941619270.07902464143020.108054966111-0.002437908171780.03941446827270.149515734476-0.00785310445026-0.01052652645360.34410274670.01472416150030.195043406181-34.312766635336.3296269514-0.601306482385
684.02243762452-3.2268284586-2.798386177147.012045915824.961790037784.11439538709-0.0311148208676-0.315743188086-0.5584478896410.761031067957-0.3337654074220.8767740541770.499236064163-0.5776044033860.4063327867350.291090618235-0.05806560060720.08661094681680.4745053162130.1277668819610.354590917193-49.216093294836.8766006297.81288485026
693.65440320357-0.261321809944-0.4444326125182.967243991040.04445956691282.168589756750.0030616667707-0.01304799151560.164126858391-0.11655275466-0.00695204948175-0.502583248776-0.1076035382930.4607517634640.01033037246160.147917254398-0.06813695170650.06261052031160.437027095882-0.01540316799870.4161134243213.9349289307559.4319366992-35.1513679208
704.177220856151.53606690201-0.7092236642571.164535243070.1035810572321.70055001632-0.2900501389850.496584372658-0.18622573066-0.2697375878420.272183820738-0.2956472337280.09057117234730.022514880275-0.01698759877450.216099921821-0.06584667856790.08139333965760.433985343457-0.01952969438910.35934247355-0.89575283344152.5671207751-42.0613057381
710.8639659234290.2648279885880.1263820788031.007189700940.2646492407932.51302457808-0.07648698486450.187831643586-0.0385643317328-0.005516056730850.0869441899321-0.09341392212670.01440674187110.160368292772-0.03053233827990.0996535291286-0.02153323395260.01094695225310.3222105256690.00496972890430.257551228853-10.647443304752.3777142729-28.6823664915
720.910740391819-1.33214751829-0.4757912267854.196482779633.806653017735.76589086705-0.316722623633-0.237345507588-0.02716073088480.4233186305340.410503261934-0.21264729280.1921971726650.821154565948-0.1262630978630.1706021975340.0143652386328-0.02613282227050.4440482173780.02624010180810.4193430406443.8249561123351.9363114793-21.9537404092
737.52065817233-1.118312634972.535143412452.86451701409-1.764563154925.56986583284-0.243749645443-0.513836215236-0.113145214625-0.1117061083370.31205205597-0.448599895797-0.0132680989582-0.0321873774910.05397422726830.172882775265-0.005900608651790.07241765740420.386124164472-0.1464927363590.324165424917-11.162718820622.2678764332-44.6552329919
746.96715613732-3.6007764371.786100604764.23662089743-0.9838055858612.408353946860.1661577024850.897478314521-0.478333923398-0.394254230585-0.0877463184-0.777723314262-0.006023977135960.465939041897-0.1015937821840.222947438591-0.03445268568020.1250858962680.380917974868-0.08434783378820.409277824948-8.1165119513823.5104906306-53.2596110324
755.48225151472-0.06372716894572.512281539252.26006942360.008834819461263.946223939440.08286730988220.0306702832503-0.268640337648-0.241339278659-0.0656466609757-0.281760554990.293425783620.1665573293140.04961745473490.1938186361280.02365500822050.09941776879210.32021400315-0.1142719196220.366390268566-14.946195122516.2579654758-51.8808312482
765.00617048749-0.4136665883942.132580720224.78762318518-0.7492974151446.177642950610.6728317134760.656159049319-0.64412825202-0.274944032857-0.183281453289-0.874023482230.5015095731210.837948884141-0.1470866900010.3582161855410.03853452003510.1002538129380.510870630872-0.2238083535720.605042114695-9.1054537338510.3886339705-53.5248193268
771.33444327752-0.204976777856-0.7796690857372.45431172445-0.1389851604512.37861016282-0.03992535167220.0379931974015-0.1426959072640.1605463861210.042866392479-0.237279714660.1696552944710.2501042694240.03023265485480.1393274182730.000276958911059-0.001844163197520.305969529593-0.0844379376680.366108717934-15.70734866717.4943014517-39.6589605616
783.225498590983.933907453485.030555721354.859262726285.940468429938.081551083920.139839835511-0.5377789591960.198568450407-0.066090857419-0.285895321635-0.04244395136620.00881797922467-0.2780243625140.2580309921660.1634022875620.02170896862750.007133594451350.2749056336150.0270946951080.314881412688-17.947377930220.4167705566-33.8402206882
794.22470826855-0.04486204306112.214598531291.13382141073-0.8617671276394.171099762540.000415777872685-0.0176891591599-0.340088542917-0.1508099118410.0786532409289-0.1117496354640.1426257397440.227698453391-0.0673443561470.183511803013-0.0009097046372440.05249033974970.209751181326-0.07856211609220.232251937647-19.087168180930.2656102555-41.7020285719
806.038554084021.751111585995.565088107843.246749627371.167795130515.49025833164-0.1714017052060.185543523638-0.380447861209-0.0636301402570.18789911666-0.169013344408-0.2811686731840.2826347653860.02925319436860.12044869451-0.001722054292550.04186494289390.293400254632-0.03991146510490.263556928348-25.249488658434.7849306189-37.3792657303
811.979840678130.5883909838952.420180823852.535877869641.513060913064.24464636485-0.06970767210330.170904768905-0.0331229324133-0.5062778010090.264872309338-0.521683151436-0.0745253460610.224988173879-0.1302511733750.1734128796580.04973372520960.09985793145320.354344679772-0.006179834877840.370115390588-12.423739666637.9510237206-53.8113582388
823.22127729624-1.452384779521.565671444371.77538925878-1.950212407412.11555724799-0.02439808537680.281025091655-0.118283378935-0.3657603167310.016498111428-0.698668054055-0.03266615242330.8543863649120.1311327323780.242526269526-0.03161144884730.141112804030.485052798765-0.07717458957290.516914250004-6.1944140154931.6999653319-52.0706634295
833.47619857351-1.209162393160.7974101553535.397481175640.01658528064855.90325957552-0.0635423726970.301145279569-0.112542892138-0.682140316925-0.009608147354270.2171370970080.0612010937194-0.3926272259920.02071946234940.339285797549-0.04411906666410.04381343266490.4460718773320.01868340589170.157079140175-28.4667055250.4724970449-63.0357249904
845.29562310769-1.077801803530.8100401608494.1481916594-2.066758124444.426823349340.2517646832090.8350631704390.120333879377-0.826719376189-0.181541378749-0.215080203042-0.03289299833620.270166377186-0.03774411456520.390053396623-0.04316876880450.1003670027660.5432240598630.0606383512020.240564160791-17.57101569756.5749585234-65.7761313167
851.09025222788-0.705969273163-1.079583158122.376174658020.126602657144.522537745340.03851012334870.3430228363890.0720962684603-0.31742342608-0.05246597021460.131271726489-0.350881441593-0.2352153947710.05830039329830.223840851507-0.0616308845304-0.03365223997920.3586588479980.03444731287280.213469992749-28.965863878758.0147880962-54.4180608209
861.03985684973-0.6884611461030.3921373759122.772443239110.5881043746750.357862838679-0.03297294577390.0607814363786-0.0449479778459-0.1932472791780.0106070980864-0.00942810347173-0.07268247611670.03951367516620.0200659525070.174921193128-0.02860520717530.03479378324190.3153352914750.007644409561950.172530357942-27.16236669844.3661000143-49.2266141011
873.89498092329-4.42912515947-1.552581463967.910189715583.228268908373.691943640720.1622729879040.815320905038-0.547791088283-0.757397950434-0.1876447424320.536775552065-0.00607834277519-0.2274361541480.08487351101440.346341992826-0.0199791735854-0.03389802621280.450669078312-0.03126747548370.182512694896-28.442535745438.8580170986-62.5614670835
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 16 )
2X-RAY DIFFRACTION2chain 'A' and (resid 17 through 29 )
3X-RAY DIFFRACTION3chain 'A' and (resid 30 through 39 )
4X-RAY DIFFRACTION4chain 'A' and (resid 40 through 57 )
5X-RAY DIFFRACTION5chain 'A' and (resid 58 through 78 )
6X-RAY DIFFRACTION6chain 'A' and (resid 79 through 96 )
7X-RAY DIFFRACTION7chain 'A' and (resid 97 through 129 )
8X-RAY DIFFRACTION8chain 'A' and (resid 130 through 144 )
9X-RAY DIFFRACTION9chain 'A' and (resid 145 through 156 )
10X-RAY DIFFRACTION10chain 'A' and (resid 157 through 174 )
11X-RAY DIFFRACTION11chain 'A' and (resid 175 through 194 )
12X-RAY DIFFRACTION12chain 'B' and (resid 1 through 16 )
13X-RAY DIFFRACTION13chain 'B' and (resid 17 through 29 )
14X-RAY DIFFRACTION14chain 'B' and (resid 30 through 57 )
15X-RAY DIFFRACTION15chain 'B' and (resid 58 through 104 )
16X-RAY DIFFRACTION16chain 'B' and (resid 105 through 144 )
17X-RAY DIFFRACTION17chain 'B' and (resid 145 through 157 )
18X-RAY DIFFRACTION18chain 'B' and (resid 158 through 174 )
19X-RAY DIFFRACTION19chain 'B' and (resid 175 through 196 )
20X-RAY DIFFRACTION20chain 'C' and (resid 2 through 16 )
21X-RAY DIFFRACTION21chain 'C' and (resid 17 through 29 )
22X-RAY DIFFRACTION22chain 'C' and (resid 30 through 57 )
23X-RAY DIFFRACTION23chain 'C' and (resid 58 through 69 )
24X-RAY DIFFRACTION24chain 'C' and (resid 70 through 144 )
25X-RAY DIFFRACTION25chain 'C' and (resid 145 through 156 )
26X-RAY DIFFRACTION26chain 'C' and (resid 157 through 174 )
27X-RAY DIFFRACTION27chain 'C' and (resid 175 through 194 )
28X-RAY DIFFRACTION28chain 'D' and (resid 1 through 16 )
29X-RAY DIFFRACTION29chain 'D' and (resid 17 through 29 )
30X-RAY DIFFRACTION30chain 'D' and (resid 30 through 57 )
31X-RAY DIFFRACTION31chain 'D' and (resid 58 through 69 )
32X-RAY DIFFRACTION32chain 'D' and (resid 70 through 104 )
33X-RAY DIFFRACTION33chain 'D' and (resid 105 through 144 )
34X-RAY DIFFRACTION34chain 'D' and (resid 145 through 157 )
35X-RAY DIFFRACTION35chain 'D' and (resid 158 through 174 )
36X-RAY DIFFRACTION36chain 'D' and (resid 175 through 195 )
37X-RAY DIFFRACTION37chain 'E' and (resid 2 through 16 )
38X-RAY DIFFRACTION38chain 'E' and (resid 17 through 29 )
39X-RAY DIFFRACTION39chain 'E' and (resid 30 through 39 )
40X-RAY DIFFRACTION40chain 'E' and (resid 40 through 57 )
41X-RAY DIFFRACTION41chain 'E' and (resid 58 through 69 )
42X-RAY DIFFRACTION42chain 'E' and (resid 70 through 129 )
43X-RAY DIFFRACTION43chain 'E' and (resid 130 through 144 )
44X-RAY DIFFRACTION44chain 'E' and (resid 145 through 156 )
45X-RAY DIFFRACTION45chain 'E' and (resid 157 through 194 )
46X-RAY DIFFRACTION46chain 'F' and (resid 2 through 16 )
47X-RAY DIFFRACTION47chain 'F' and (resid 17 through 69 )
48X-RAY DIFFRACTION48chain 'F' and (resid 70 through 129 )
49X-RAY DIFFRACTION49chain 'F' and (resid 130 through 174 )
50X-RAY DIFFRACTION50chain 'F' and (resid 175 through 196 )
51X-RAY DIFFRACTION51chain 'G' and (resid 2 through 57 )
52X-RAY DIFFRACTION52chain 'G' and (resid 58 through 69 )
53X-RAY DIFFRACTION53chain 'G' and (resid 70 through 104 )
54X-RAY DIFFRACTION54chain 'G' and (resid 105 through 144 )
55X-RAY DIFFRACTION55chain 'G' and (resid 145 through 156 )
56X-RAY DIFFRACTION56chain 'G' and (resid 157 through 174 )
57X-RAY DIFFRACTION57chain 'G' and (resid 175 through 196 )
58X-RAY DIFFRACTION58chain 'H' and (resid 2 through 29 )
59X-RAY DIFFRACTION59chain 'H' and (resid 30 through 57 )
60X-RAY DIFFRACTION60chain 'H' and (resid 58 through 69 )
61X-RAY DIFFRACTION61chain 'H' and (resid 70 through 129 )
62X-RAY DIFFRACTION62chain 'H' and (resid 130 through 144 )
63X-RAY DIFFRACTION63chain 'H' and (resid 145 through 156 )
64X-RAY DIFFRACTION64chain 'H' and (resid 157 through 174 )
65X-RAY DIFFRACTION65chain 'H' and (resid 175 through 194 )
66X-RAY DIFFRACTION66chain 'I' and (resid 2 through 78 )
67X-RAY DIFFRACTION67chain 'I' and (resid 79 through 174 )
68X-RAY DIFFRACTION68chain 'I' and (resid 175 through 196 )
69X-RAY DIFFRACTION69chain 'J' and (resid 2 through 69 )
70X-RAY DIFFRACTION70chain 'J' and (resid 70 through 104 )
71X-RAY DIFFRACTION71chain 'J' and (resid 105 through 174 )
72X-RAY DIFFRACTION72chain 'J' and (resid 175 through 196 )
73X-RAY DIFFRACTION73chain 'K' and (resid 2 through 16 )
74X-RAY DIFFRACTION74chain 'K' and (resid 17 through 29 )
75X-RAY DIFFRACTION75chain 'K' and (resid 30 through 57 )
76X-RAY DIFFRACTION76chain 'K' and (resid 58 through 69 )
77X-RAY DIFFRACTION77chain 'K' and (resid 70 through 118 )
78X-RAY DIFFRACTION78chain 'K' and (resid 119 through 129 )
79X-RAY DIFFRACTION79chain 'K' and (resid 130 through 144 )
80X-RAY DIFFRACTION80chain 'K' and (resid 145 through 157 )
81X-RAY DIFFRACTION81chain 'K' and (resid 158 through 174 )
82X-RAY DIFFRACTION82chain 'K' and (resid 175 through 197 )
83X-RAY DIFFRACTION83chain 'L' and (resid 2 through 39 )
84X-RAY DIFFRACTION84chain 'L' and (resid 40 through 69 )
85X-RAY DIFFRACTION85chain 'L' and (resid 70 through 118 )
86X-RAY DIFFRACTION86chain 'L' and (resid 119 through 174 )
87X-RAY DIFFRACTION87chain 'L' and (resid 175 through 194 )

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more