[English] 日本語
Yorodumi
- PDB-7wsb: The ternary complex structure of FtmOx1 with a-ketoglutarate and ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7wsb
TitleThe ternary complex structure of FtmOx1 with a-ketoglutarate and 13-oxo-fumitremorgin B
ComponentsVerruculogen synthase
KeywordsOXIDOREDUCTASE / dioxygenase / non-heme / iron dependent
Function / homology
Function and homology information


verruculogen synthase / verruculogen biosynthetic process / dioxygenase activity
Similarity search - Function
Phytanoyl-CoA dioxygenase / Phytanoyl-CoA dioxygenase (PhyH)
Similarity search - Domain/homology
13-Oxofumitremorgin B / 2-OXOGLUTARIC ACID / : / DI(HYDROXYETHYL)ETHER / Verruculogen synthase
Similarity search - Component
Biological speciesAspergillus fumigatus Af293 (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.87 Å
AuthorsWang, J. / Wang, X.Y. / Wang, Y.Y. / Yan, W.P.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Jacs Au / Year: 2022
Title: Dissecting the Mechanism of the Nonheme Iron Endoperoxidase FtmOx1 Using Substrate Analogues.
Authors: Zhu, G. / Yan, W. / Wang, X. / Cheng, R. / Naowarojna, N. / Wang, K. / Wang, J. / Song, H. / Wang, Y. / Liu, H. / Xia, X. / Costello, C.E. / Liu, X. / Zhang, L. / Liu, P.
History
DepositionJan 28, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 6, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 17, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Verruculogen synthase
B: Verruculogen synthase
C: Verruculogen synthase
D: Verruculogen synthase
E: Verruculogen synthase
F: Verruculogen synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)219,54328
Polymers215,0516
Non-polymers4,49222
Water2,468137
1
A: Verruculogen synthase
B: Verruculogen synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,35311
Polymers71,6842
Non-polymers1,6699
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5080 Å2
ΔGint-28 kcal/mol
Surface area22890 Å2
MethodPISA
2
C: Verruculogen synthase
D: Verruculogen synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,1419
Polymers71,6842
Non-polymers1,4577
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5170 Å2
ΔGint-30 kcal/mol
Surface area22760 Å2
MethodPISA
3
E: Verruculogen synthase
F: Verruculogen synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,0498
Polymers71,6842
Non-polymers1,3656
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5240 Å2
ΔGint-32 kcal/mol
Surface area22070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.050, 85.447, 160.768
Angle α, β, γ (deg.)90.000, 108.838, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
Components

-
Protein , 1 types, 6 molecules ABCDEF

#1: Protein
Verruculogen synthase / Fumitremorgin biosynthesis protein F


Mass: 35841.812 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus fumigatus Af293 (mold) / Strain: Af293 / Gene: ftmOx1, ftmF, AFUA_8G00230 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q4WAW9, verruculogen synthase

-
Non-polymers , 6 types, 159 molecules

#2: Chemical
ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Co
#3: Chemical
ChemComp-4IL / 13-Oxofumitremorgin B / (1R,12S,15S)-1-hydroxy-7-methoxy-10-(3-methylbut-2-enyl)-12-(2-methylprop-1-enyl)-10,13,19-triazapentacyclo[11.7.0.03,11.04,9.015,19]icosa-3(11),4(9),5,7-tetraene-2,14,20-trione


Mass: 477.552 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C27H31N3O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-AKG / 2-OXOGLUTARIC ACID / Α-Ketoglutaric acid


Mass: 146.098 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C5H6O5
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 137 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.15 Å3/Da / Density % sol: 60.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M MES/Imidazole pH 6.5, 20% PEG 500 MME, 10% PEG 20,000, 0.03 M MgCl2, 0.03 M CaCl2
PH range: 6.0-7.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97852 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 20, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97852 Å / Relative weight: 1
ReflectionResolution: 2.87→30 Å / Num. obs: 60482 / % possible obs: 98.5 % / Redundancy: 6.4 % / Biso Wilson estimate: 51.93 Å2 / CC1/2: 0.98 / Rsym value: 0.14 / Net I/σ(I): 13.39
Reflection shellResolution: 2.87→2.92 Å / Mean I/σ(I) obs: 2.44 / Num. unique obs: 2949 / CC1/2: 0.838 / Rsym value: 0.608

-
Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4Y5T
Resolution: 2.87→30 Å / SU ML: 0.2851 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.8728
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.211 1993 3.3 %
Rwork0.1608 58415 -
obs0.1624 60408 98.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 52.77 Å2
Refinement stepCycle: LAST / Resolution: 2.87→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13551 0 302 137 13990
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004914240
X-RAY DIFFRACTIONf_angle_d0.793919436
X-RAY DIFFRACTIONf_chiral_restr0.05322144
X-RAY DIFFRACTIONf_plane_restr0.00462569
X-RAY DIFFRACTIONf_dihedral_angle_d21.78965494
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.87-2.940.26011340.21614027X-RAY DIFFRACTION94.98
2.94-3.020.24251380.19764076X-RAY DIFFRACTION98.18
3.02-3.110.28311400.20584141X-RAY DIFFRACTION97.61
3.11-3.210.23831470.20254192X-RAY DIFFRACTION98.5
3.21-3.320.25491390.19284101X-RAY DIFFRACTION97.81
3.32-3.460.21751410.17084165X-RAY DIFFRACTION98.42
3.46-3.610.23671460.16524152X-RAY DIFFRACTION98.76
3.61-3.80.20671400.16484161X-RAY DIFFRACTION98.08
3.8-4.040.23171430.15334249X-RAY DIFFRACTION99.68
4.04-4.350.18421460.1354236X-RAY DIFFRACTION99.5
4.35-4.790.17481450.12134221X-RAY DIFFRACTION98.98
4.79-5.480.15181440.14364197X-RAY DIFFRACTION98.91
5.48-6.880.25791430.17034242X-RAY DIFFRACTION98.96
6.88-29.250.18381470.15484255X-RAY DIFFRACTION97.05
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)
10.7999834084350.510265439090.03103754725070.907859234869-0.5682819244160.814475442845-0.2437522482450.0398335505817-0.853101954733-0.02705851691480.158843782154-0.2878045720340.8980640915440.211735875648-0.001773029496770.4692816146350.03533414186740.05300565078630.403837984212-0.08613424839580.573708705986-23.9159972886-39.505584107551.7959080264
20.195825171952-0.2960746057110.1852795045780.656554455384-0.1388548840140.364978939279-0.3784846374690.207456673708-0.670990737489-0.3683653628761.215861115211.211398875060.0238030543506-1.011064530810.01600071726340.378750870174-0.0333333799366-0.007522016108230.6276829453060.04217686613430.650386744595-46.2652059996-26.766348298254.3415596166
32.040040432530.747345440909-0.3648176022891.259535175850.2106683931890.899578865108-0.1684824820850.4429383871910.131724202795-0.1649406293640.1293722235370.100295570436-0.14712298832-0.2435528866480.00129744498290.3280550956610.03396784164510.05371867279070.3839167095140.01237751082720.41466550753-32.9609580989-20.455987998453.6146749805
40.7142716200290.365701943379-0.6915283154880.9411658383870.08841450340720.9144489039760.09213332260140.528505444453-0.0731435612876-0.3523523076580.000996965282060.04437147151850.083331305881-0.114112638776-5.99282900799E-70.3502481840130.04355125839750.01274231001660.4395614975570.00822282382660.452293348883-22.4422830368-22.490386173146.2633587387
50.2397801769130.0490905870079-0.009017926828490.5707237386080.1388627286620.950149882459-0.3453272075221.04717826811-0.472316235754-0.419032328163-0.00343471399378-0.09347314473020.2369267156790.146970843007-9.4062114451E-70.5042515183650.04689529788160.02591247214270.650578536109-0.08554116701950.490387715348-25.3980153428-30.58088695638.3269847962
61.533856613710.1849824330230.03002021449711.627165203970.4717318570122.56395662663-0.003806726804230.272780863981-0.03001099811810.01689832517550.01519333031680.1890678795190.094340068078-0.1992385324676.6203366329E-100.2807274332540.02973397439950.01246084830480.2646307578980.05035827212880.412956378097-28.9329117321-21.707099591556.9119032681
73.874931023222.103628576840.9502013420932.488762411270.6375051524030.4044477607230.476875466584-0.955075462028-0.1218160181770.531973329943-0.607987108319-0.162188293848-0.202592191975-0.176580619815-0.002215056044160.436679975464-0.01540122769260.102448576680.315176676897-0.0006200272247420.459609995985-29.3112911664-14.488958834177.0231270987
83.78099417852-1.162437905562.766735921031.84786861197-0.2642491462162.265109320050.4493116234690.8995315455930.533606876091-0.678745015881-0.270284762376-0.392433294858-0.3228589839220.6028516952140.3586266430480.46376028054-0.01340827463280.2078005283030.3085945431710.09891068399130.6241115961782.512085567186.3212032525155.53039167
90.0919239101049-0.03011625391240.1143956179930.0368052825266-0.1538773228370.587986161264-0.0157174842013-0.1842093967010.1270968309580.6273473186360.147034975462-0.710062234538-1.071156708390.171654807456-0.004138601906240.519063556349-0.03449413956630.10301521580.335478961457-0.0447841021820.545013723236-12.52518892911.792660514876.635295468
102.324163204910.1343122258820.06572763604661.356985580050.5456507488330.4975294356360.133237537718-0.05127904146680.1382970388080.0929245060707-0.0325628463827-0.19319594004-0.0303828539582-0.01124363638081.67099074375E-50.3578430336410.003792439312840.08294650991150.2383798452840.03472925791060.390255577893-10.3280109354-3.1949732928866.8248709101
111.48527649591-0.15685814554-0.1163867431261.666737250870.005673717597861.577463235430.493020206724-0.2613626652720.14440226060.0559530927725-0.105770059518-1.170441295090.1115236674840.2983628716370.02557215489340.330681720882-0.04620697963650.07910528241340.372634151935-0.01812495389620.5466974883245.89516002411-4.2989736402266.7386241091
122.351007011830.1521467936910.1810378634261.45191053331-0.1326690455741.594897719650.1583393490490.09290881447390.394839150228-0.06550415485990.005989997927630.0037046658844-0.130447920863-0.05403353957840.001800622316070.3503568189150.0110383778670.1167780067050.1727939421660.0549873958650.410466791243-14.4319271842-0.76725969025763.2685822818
131.845232507710.9558629767991.220457388382.866600815582.282654968891.96143221703-0.05209769824980.124246810250.582361537304-1.56694632903-0.03252319905150.487142901389-0.849028399084-0.436168839731-0.02023293891490.4731802710950.1500650485360.02625349673810.4427681719470.1683973982950.734203494389-34.18194822642.3681783385656.0489126081
140.8809291314050.523861167519-0.3144962876922.085115168951.089170421923.29566323817-0.3013944131980.007861474984120.44521580005-0.01975279190320.259332002999-0.0871699458962-0.4582055828440.00208564687532-6.20033693165E-50.361645192131-0.0374497068334-0.01338778663550.3229526890510.0906201748210.46139924051131.5978532778-8.9113595402252.6722312299
151.6045703840.04650407888550.5691496252720.53904355049-0.1936560036480.624967218241-0.02314362560770.48972852285-0.0612800626143-0.2207936394410.0499331727477-0.09611709052850.04689234756530.1392351045280.0003649861092530.3627798592580.0216577839073-0.01318219868160.406733095326-0.02862495276880.44042337864229.3663073799-22.9230605751.0301376383
160.471909511954-0.44142547526-0.02647870620810.851983707615-0.3100843172281.16328410785-0.443779023690.8875093701620.545727243327-0.4449874016820.004877512265580.190491826087-0.0864902013671-0.0914189505583-8.36851428016E-70.5135407212480.00528295330767-0.03571578740410.6894599099560.0533244008960.47820025693225.4580303841-13.510219182538.2955765947
171.68429261040.1421179891210.09018475200651.71237475707-0.5258931628412.40993292816-0.01252750813360.29078388822-0.02779821166450.0104575739912-0.000188720669435-0.136803885285-0.1227378233330.1731071230216.16315990113E-90.2776465504840.0301418254599-0.02176520364610.256291514601-0.05207738572440.38730489513529.0212786395-22.383084988556.9199498641
183.810811948272.00340799124-0.376765865132.95173493363-0.5141896183960.4214999532660.498739113216-1.06411987472-0.1750922743920.730337421371-0.694579357911-0.09318533282640.09592635950980.0215119058988-0.06467606939580.412767069869-0.0538696689797-0.09032910766970.271684236060.005823047959950.44317439018529.4243908858-29.592162443377.0207624179
192.62865037024-1.01633072798-1.466729884471.01240649024-0.2231795843331.857017147660.2798722881450.797054834753-0.519579222215-0.75954255809-0.1725758590960.4195828486350.442376855602-0.4630140649010.09964374609030.458257884070.00150429300232-0.1941918148680.361209244299-0.07817538683690.611470125593-2.45984161031-50.445035540755.4783156334
200.446770627870.0975741247654-0.151752533270.4360895051270.7546856533951.52840379404-0.0447788642246-0.118676773786-0.1435999139630.627177711207-0.002781049719270.7717008115331.13452745051-0.191097284006-0.01643948003630.588823901627-0.0423554570171-0.08800370044870.2262850015950.06468011648050.62471505701412.6326634107-55.909486289976.6272368327
212.515441049940.2772294905440.3412211489011.81645281289-0.6986424882410.6677236810480.14045667712-0.155641029848-0.08935714227130.13841272488-0.1333379118390.1155462255050.0157872469955-0.106454718987-1.02245471964E-80.33016738424-0.00159497028802-0.08666027636430.203264986425-0.03336780746670.44129028976213.5675191069-43.661917528568.6522388201
222.380158142090.4499486889150.09532944275931.156060828370.1952949089230.02378490047990.04687599724440.126773767747-0.0478656391428-0.0131797386390.08423441153710.196114287891-0.0803998343287-0.105211050469-1.09957063796E-60.3459205112520.0219156466837-0.07898851163570.227096225295-0.004517082728540.4055519614584.58638047908-35.763056059963.3819737616
231.11059556315-0.4881832641140.527410592332.33556330935-0.6881405961051.785000985110.398767639865-0.369899576222-0.09075499300490.2560920032610.0840074294491.1268643215-0.124336937707-0.4549580221540.04695293671080.341378629934-0.0357953502303-0.07912125172870.3956245119350.04058612672470.546768388647-5.76183901244-39.780270088166.810087154
242.305859104120.377893027676-0.00767118676541.36840007649-0.1067955694131.163910752480.2168505843820.0639048460574-0.358285376855-0.0824462025242-0.04687613072570.009005804425160.1129862664810.03878970161820.001378085815570.3493606842040.00149857544295-0.0979082116080.179396419552-0.0549629732140.42102826411214.5212638651-43.31711746363.2805374696
250.9162340850010.6939419554860.1021267374671.13540901998-0.7789618731371.194365989050.1022895937920.179762003645-0.695028027371-1.2959511554-0.138174021404-0.4962784577250.7163094025020.326445426394-0.0332793593820.4228488726550.123743096328-0.04289977426360.442834171824-0.1564742835840.67548714348534.2654110291-46.50186778356.0573549799
260.3096765706440.3564920002-0.07013330522620.8164584348140.1340212340610.2844518164810.188174839245-0.0741599455890.3354420935350.1946518158950.137619545436-0.250160120873-1.100363703720.863768614224-5.53224956137E-80.84262647797-0.13766451180.1813052950840.9005540873890.08523594787230.5937593176448.618123567943.2453794275230.8080752197
271.72158029903-0.9801875410780.4721132322310.90182323674-0.00121249049050.3330615946640.1249148338970.9505320872310.784882480614-0.3197377999360.133849380805-0.0263663585133-1.12182574405-0.1478565116270.05665229889181.103749681840.1030212972140.1079919006310.9830224594080.2190813545760.436780904784-2.139263774415.295251357567.36458937352
280.262141987291-0.1125148923620.4872563202751.931094307050.5950327306041.229014783680.2245707863060.3198664468930.0213085378753-0.208567082618-0.1256851437210.248011321977-0.3643681976730.02776712937317.12482921159E-50.7103282122280.1005478729230.08497391942330.9129926409270.1205643742670.379927450425-2.62962655923-6.6115304842815.772773341
29-0.00391921043146-0.0131856644749-0.0128805106710.6735698029790.7933668945410.9235146251790.1733169415880.6123032650330.209585869551-0.239927244221-0.01038682447360.399994146918-0.147205033733-0.302957762767-1.49082624451E-60.6296520746170.1188014439490.003665125510590.8991869771850.03232255860970.504182165113-9.79379324013-7.7117302477827.8508053792
300.80566696077-0.3117176208420.1939669212151.72998657803-0.6598463328241.567696259320.326264444684-0.3713940926590.05458175300270.4058510009690.03891239349540.12952917446-0.860132369170.17804146124-0.02414569569970.4879267879270.08301069474390.1061710126130.7605552168870.1198544566330.2664404673282.94250213786-9.7951375397829.36206068
310.7787964785290.5043512358150.3971095488930.6593491130050.3920045990380.5904186003980.383984675163-0.07347690911130.2461806257650.160811074492-0.1601783991960.357958593055-0.891114242888-0.160430244518-4.0057622198E-70.7539595773380.1092357654710.0992053659630.7361807954530.09830707411030.458425143453-7.224120539792.0321888612333.1319139081
320.5099343611770.0631277231211-0.1354717474172.355915842831.097138057281.527117835990.2109824488920.3278421058350.187413003394-0.41091210244-0.214143908224-0.00365782364542-0.440624815040.144791029153-0.01593180369150.6168566206160.1058040065130.05031813877570.9008495682430.1366942741530.3408896935691.71659651418-8.9741361578417.7590659286
330.1775106806730.2740718179730.2014151478053.30355455781-0.6609125707530.5447463189390.2560425686230.158805294622-0.200835171712-0.59421408432-0.59597141038-1.13722555021-0.05915623120050.231341345951-0.03380087763210.8020867788560.1406485773610.1889765285331.093858570280.04062752862440.50927136093914.0076862093-20.72222961994.97219472717
340.6436660209770.7475923894950.002745334897031.03738165578-0.222048464330.4337012735830.4025399362170.0142236241613-0.3546058072260.14952348724-0.03798058872150.4300979070961.25208278397-0.9227569069342.38068035326E-70.846031153088-0.11503965529-0.1521827630980.842252960811-0.04415785727940.618667597909-8.39366604484-47.562353058231.0702414085
354.4224765516-1.66942302831-1.316578628191.08108758345-0.03451962279921.0153336780.04903368292080.479264503246-0.990963904842-0.625912111381-0.009243501449730.06604589936551.441331130340.236183186855-0.03208130026641.163815325220.112002910068-0.1486556895371.04935253529-0.2262953379350.4274374809962.1997936945-49.37750540357.34424463126
360.378001139492-0.291057453887-0.7477413362931.73934694935-0.1824594389161.73329023070.2495602579170.2774806502530.109991274739-0.266923282823-0.127790209663-0.1723459419850.354153228911-0.143047821393-4.1332815015E-80.6897992379270.114713569047-0.08569975297190.860962771923-0.09302324628140.4127940188812.64901512938-37.495948041815.7740136459
370.5070739356860.06593760501560.5490514404311.054070065-0.5350303776540.9348290820570.3719913464480.402076147482-0.174169322641-0.439588893781-0.269665002435-0.213420828880.1909988375560.2331268314455.41319076658E-50.5640117726440.0796567337035-0.01462790641560.866937130203-0.0585215438260.3476675490714.88600875601-35.530011173128.4100848159
380.43698716195-0.1391505125240.1798617529910.364945080458-0.28227273250.4225728227410.350603138394-0.0751712688654-0.210182348668-0.0854816701517-0.0559556256709-0.4065879977020.5823499585930.01042778393630.003209355256120.7249468666470.0659069861092-0.03041718768150.746082201262-0.1063750491310.4694032510667.33396685473-46.107007455933.1650200907
390.9611617032740.932898376054-0.5443502122041.31495951448-0.9646358298560.7667906044080.1108479094620.21555930255-0.257349490732-0.283819499838-0.128212654736-0.336393206050.608496241475-0.122761808143-0.002005411541480.7033731817680.0916259938861-0.06914625714950.836327791258-0.1368075160860.3937282584273.3624128371-41.323029023921.495475705
400.6831407994050.1061884198370.2291260977071.28908382985-0.8483596728740.796811836050.2405931198710.341286707734-0.224283202722-0.430532113028-0.1459736535210.5545359964870.223963358356-0.163322204469-0.00761168716990.660820419890.181594200031-0.1147823259671.07292391316-0.08768253058030.419903005583-10.8456627352-24.55911398179.85180893983
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 6 through 38 )AA6 - 381 - 33
22chain 'A' and (resid 39 through 54 )AA39 - 5434 - 49
33chain 'A' and (resid 55 through 119 )AA55 - 11950 - 114
44chain 'A' and (resid 120 through 155 )AA120 - 155115 - 150
55chain 'A' and (resid 156 through 185 )AA156 - 185151 - 180
66chain 'A' and (resid 186 through 274 )AA186 - 274181 - 271
77chain 'A' and (resid 275 through 290 )AA275 - 290272 - 287
88chain 'B' and (resid 4 through 38 )BE4 - 381 - 35
99chain 'B' and (resid 39 through 54 )BE39 - 5436 - 51
1010chain 'B' and (resid 55 through 155 )BE55 - 15552 - 152
1111chain 'B' and (resid 156 through 185 )BE156 - 185153 - 182
1212chain 'B' and (resid 186 through 274 )BE186 - 274183 - 271
1313chain 'B' and (resid 275 through 290 )BE275 - 290272 - 287
1414chain 'C' and (resid 6 through 54 )CI6 - 541 - 49
1515chain 'C' and (resid 55 through 155 )CI55 - 15550 - 150
1616chain 'C' and (resid 156 through 185 )CI156 - 185151 - 180
1717chain 'C' and (resid 186 through 274 )CI186 - 274181 - 271
1818chain 'C' and (resid 275 through 290 )CI275 - 290272 - 287
1919chain 'D' and (resid 4 through 38 )DM4 - 381 - 35
2020chain 'D' and (resid 39 through 54 )DM39 - 5436 - 51
2121chain 'D' and (resid 55 through 119 )DM55 - 11952 - 116
2222chain 'D' and (resid 120 through 155 )DM120 - 155117 - 152
2323chain 'D' and (resid 156 through 185 )DM156 - 185153 - 182
2424chain 'D' and (resid 186 through 274 )DM186 - 274183 - 271
2525chain 'D' and (resid 275 through 290 )DM275 - 290272 - 287
2626chain 'E' and (resid 6 through 38 )EQ6 - 381 - 33
2727chain 'E' and (resid 39 through 54 )EQ39 - 5434 - 49
2828chain 'E' and (resid 55 through 119 )EQ55 - 11950 - 114
2929chain 'E' and (resid 120 through 140 )EQ120 - 140115 - 135
3030chain 'E' and (resid 141 through 155 )EQ141 - 155136 - 150
3131chain 'E' and (resid 156 through 185 )EQ156 - 185151 - 180
3232chain 'E' and (resid 186 through 274 )EQ186 - 274181 - 271
3333chain 'E' and (resid 275 through 290 )EQ275 - 290272 - 287
3434chain 'F' and (resid 5 through 38 )FU5 - 381 - 34
3535chain 'F' and (resid 39 through 54 )FU39 - 5435 - 50
3636chain 'F' and (resid 55 through 119 )FU55 - 11951 - 115
3737chain 'F' and (resid 120 through 155 )FU120 - 155116 - 151
3838chain 'F' and (resid 156 through 185 )FU156 - 185152 - 181
3939chain 'F' and (resid 186 through 240 )FU186 - 240182 - 238
4040chain 'F' and (resid 241 through 289 )FU241 - 289239 - 287

+
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