[English] 日本語
Yorodumi
- PDB-4y0e: X-ray Crystal Structure of a putative dioxygenase from Mycobacter... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4y0e
TitleX-ray Crystal Structure of a putative dioxygenase from Mycobacterium abscessus
ComponentsPutative dioxygenase
KeywordsOXIDOREDUCTASE / dioxygenase / Mycobacterium abscessus / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


dioxygenase activity / metal ion binding
Similarity search - Function
Clavaminate synthase-like / Double-stranded beta-helix / TauD/TfdA-like domain / Taurine catabolism dioxygenase TauD, TfdA family / Taurine dioxygenase TauD-like superfamily / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Putative dioxygenase
Similarity search - Component
Biological speciesMycobacterium abscessus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: to be published
Title: X-ray Crystal Structure of a putative dioxygenase from Mycobacterium abscessus
Authors: Fairman, J.W. / Abendroth, J. / Lorimer, D. / Edwards, T.E. / SSGCID
History
DepositionFeb 6, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative dioxygenase
B: Putative dioxygenase
C: Putative dioxygenase
D: Putative dioxygenase
E: Putative dioxygenase
F: Putative dioxygenase
G: Putative dioxygenase
H: Putative dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)304,57932
Polymers301,2808
Non-polymers3,29924
Water35,6701980
1
A: Putative dioxygenase
B: Putative dioxygenase
C: Putative dioxygenase
D: Putative dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,28916
Polymers150,6404
Non-polymers1,64912
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11200 Å2
ΔGint-113 kcal/mol
Surface area43730 Å2
MethodPISA
2
E: Putative dioxygenase
F: Putative dioxygenase
hetero molecules

G: Putative dioxygenase
H: Putative dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,28916
Polymers150,6404
Non-polymers1,64912
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area11220 Å2
ΔGint-76 kcal/mol
Surface area44200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.900, 92.980, 136.980
Angle α, β, γ (deg.)90.000, 96.110, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
31chain C
41chain D
51chain E
61chain F
71chain G
81chain H

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain AA3 - 315
211chain BB3 - 315
311chain CC3 - 500
411chain DD1 - 315
511chain EE1 - 316
611chain FF3 - 312
711chain GG3 - 500
811chain HH3 - 315

-
Components

-
Protein , 1 types, 8 molecules ABCDEFGH

#1: Protein
Putative dioxygenase /


Mass: 37660.043 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium abscessus (bacteria) / Strain: ATCC 19977 / DSM 44196 / Gene: MAB_4209c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B1MIR1

-
Non-polymers , 5 types, 2004 molecules

#2: Chemical
ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Fe
#3: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical
ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1980 / 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: 2.18 Å3/Da / Density % sol: 43.67 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Mopheus A12: 0.06 M divalents (MgCl2, CaCl2), 0.1 M TRIS/Bicine pH 8.50, 37.5% v/v MPD + PEG 1000 + PEG 3350
PH range: 8.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 24, 2011
RadiationMonochromator: Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 201264 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 4.25 % / Biso Wilson estimate: 18.73 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.067 / Rrim(I) all: 0.076 / Χ2: 0.967 / Net I/σ(I): 17.18 / Num. measured all: 855962
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.9-1.950.8540.4963.156287014988146440.56597.7
1.95-20.9060.3923.976135814635143140.44797.8
2-2.060.9390.3045.045999714271139890.34698
2.06-2.120.950.2665.755838713884136280.30398.2
2.12-2.190.970.2117.055630913365131350.2498.3
2.19-2.270.9790.1768.45492213027128220.20198.4
2.27-2.360.9830.1519.695291012530123620.17298.7
2.36-2.450.9880.12911.195090112064118980.14798.6
2.45-2.560.9910.10813.174872411550114150.12398.8
2.56-2.690.9940.08915.694678411090109720.10298.9
2.69-2.830.9960.07418.334451410545104510.08599.1
2.83-30.9970.05922.8141986997498910.06799.2
3-3.210.9980.04727.339326937092990.05499.2
3.21-3.470.9990.03733.1736616876687110.04299.4
3.47-3.80.9990.03238.0933323802779860.03699.5
3.8-4.250.9990.02743.0830047732172860.03199.5
4.25-4.910.9990.02248.6326084643564010.02599.5
4.91-6.0110.02443.7423205546754480.02799.7
6.01-8.510.02243.2818094427242610.02599.7
8.510.01550.219605239723510.01898.1

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GY9
Resolution: 1.9→45.401 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 19.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1952 9508 4.96 %RANDOM
Rwork0.1598 182187 --
obs0.1616 191695 93.99 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 100.95 Å2 / Biso mean: 28.3718 Å2 / Biso min: 6.15 Å2
Refinement stepCycle: final / Resolution: 1.9→45.401 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18680 0 192 1980 20852
Biso mean--67.63 32.57 -
Num. residues----2414
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00719673
X-RAY DIFFRACTIONf_angle_d1.07126935
X-RAY DIFFRACTIONf_chiral_restr0.0473042
X-RAY DIFFRACTIONf_plane_restr0.0053487
X-RAY DIFFRACTIONf_dihedral_angle_d12.967067
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A10750X-RAY DIFFRACTION5.437TORSIONAL
12B10750X-RAY DIFFRACTION5.437TORSIONAL
13C10750X-RAY DIFFRACTION5.437TORSIONAL
14D10750X-RAY DIFFRACTION5.437TORSIONAL
15E10750X-RAY DIFFRACTION5.437TORSIONAL
16F10750X-RAY DIFFRACTION5.437TORSIONAL
17G10750X-RAY DIFFRACTION5.437TORSIONAL
18H10750X-RAY DIFFRACTION5.437TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-1.92150.27892500.22835439568984
1.9215-1.94420.23692760.21525495577185
1.9442-1.96790.2492920.20155626591887
1.9679-1.99280.23942920.19975642593487
1.9928-2.0190.24023030.18615750605389
2.019-2.04670.21493150.1825772608790
2.0467-2.07590.23562750.17615803607890
2.0759-2.10690.22043500.17665787613791
2.1069-2.13980.21923060.16895926623292
2.1398-2.17490.18763100.15635966627692
2.1749-2.21240.1992990.15476026632593
2.2124-2.25260.20123070.1635946625393
2.2526-2.29590.22023030.16076054635794
2.2959-2.34280.21543110.16196034634594
2.3428-2.39370.19873470.15176097644495
2.3937-2.44940.19743130.15846127644095
2.4494-2.51070.20243220.15396128645095
2.5107-2.57850.18252750.15926220649596
2.5785-2.65440.22142850.16386231651696
2.6544-2.74010.20723530.16596219657297
2.7401-2.8380.21362990.16076277657697
2.838-2.95160.19013510.16296298664998
2.9516-3.08590.19313350.16326326666198
3.0859-3.24860.20683550.16796352670798
3.2486-3.4520.19363470.15196385673299
3.452-3.71840.16823480.14446400674899
3.7184-4.09240.16083620.13766405676799
4.0924-4.68410.15043640.12146418678299
4.6841-5.89940.183250.15226529685499
5.8994-45.41360.20293380.18276509684798
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)
12.06690.33870.11160.6383-0.7161.34680.1194-0.5235-0.38180.29040.06410.38120.343-0.48070.01440.2553-0.10650.01680.40060.15680.3784-57.446-2.7776133.8089
21.8410.04360.45680.6366-0.10260.96160.0678-0.4639-0.06860.2189-0.0150.1260.0597-0.26370.00310.1424-0.03190.01270.24980.02880.1472-46.84748.3475131.9695
32.5323-0.12540.64830.1022-0.38061.23620.1043-0.43970.08970.108-0.03740.511-0.0409-0.3108-0.04850.0856-0.0210.00460.235-0.05770.4465-77.393719.4465113.2079
41.39450.38150.29041.45390.45191.1690.02650.20720.0821-0.54950.04140.3811-0.0079-0.0395-0.06640.1687-0.0045-0.11890.1948-0.02320.3238-72.133314.542798.4768
51.43190.83170.44932.2012-0.26910.4265-0.00120.072-0.0921-0.28190.0443-0.07510.1150.0375-0.02670.11950.0131-0.02430.1227-0.02350.1902-56.43917.8782104.6429
60.9498-0.23530.27293.00581.91823.0286-0.19140.4081-0.4957-0.22950.133-0.26860.42160.2672-0.05620.24710.00860.07970.204-0.07640.337-46.889922.761296.8467
72.37760.770.32612.28210.12750.8778-0.06480.072-0.1028-0.1256-0.01680.07350.00520.00390.00930.1060.0005-0.00520.09920.00330.1293-51.723528.9887105.5105
81.23190.6740.13811.59110.14380.5381-0.020.0838-0.0224-0.18720.060.0941-0.0219-0.0203-0.0250.08990.0116-0.01610.1258-0.02520.1448-56.960519.9753104.4042
92.39940.0303-1.05060.45720.27920.68250.0313-0.5997-0.17110.5420.2358-0.5875-0.01750.61830.0940.08530.0014-0.0950.2736-0.06880.30372.648929.8609122.7502
103.25460.2644-2.15530.4434-0.60233.12290.2381-0.11770.09760.0510.0252-0.4854-0.12280.5523-0.02260.07730.01650.03620.2124-0.06060.27186.572527.2933112.7199
111.70230.0951-0.12720.7338-0.25062.10890.09550.1226-0.0209-0.29040.0217-0.175-0.05560.2277-0.09070.16010.00350.06860.117-0.02390.1435-0.460331.1512104.0191
120.61220.1314-0.09851.03560.38150.22080.03430.14950.0242-0.31490.0691-0.0611-0.048-0.0155-0.08010.14710.01520.01120.1193-0.00040.0892-14.353127.2264109.2099
130.85670.6788-0.2960.6285-0.22870.1737-0.24760.23830.2749-0.25720.01160.0084-0.3274-0.24780.00880.3319-0.0123-0.1230.2170.03540.2059-23.563424.4724103.23
140.879-0.41340.28782.6962-2.12352.4143-0.18810.33250.1522-0.31260.16110.1774-0.0927-0.195-0.00980.2513-0.05-0.0930.27150.03420.1687-20.971823.789798.9841
150.61530.1149-0.3911.0632-0.12970.75610.01240.0735-0.0005-0.13020.03730.008-0.0074-0.0638-0.03950.09690.0096-0.01290.09520.00130.0538-17.007227.5857112.3143
160.61440.5234-0.60991.2037-1.18682.3518-0.14690.0432-0.2754-0.37050.0759-0.14580.40460.0385-0.05080.25770.00550.03470.1464-0.05260.1412-11.103611.6199104.4175
170.570.9103-0.67386.54320.00451.1113-0.02370.1180.1992-0.6026-0.00270.0997-0.49360.04680.00910.2556-0.0203-0.01170.1280.00950.1353-19.212660.8668116.6537
180.9105-0.41841.18971.05420.23682.2307-0.0335-0.18120.22290.1226-0.05490.0855-0.1028-0.12460.07370.1287-0.0228-0.00470.1268-0.05770.1153-19.284658.9638132.8793
191.38660.04320.23030.95640.26440.29750.048-0.28870.03420.1568-0.01910.11540.096-0.0939-0.01550.1304-0.00350.00070.1629-0.0260.1136-27.257944.1349129.3201
202.8042-2.40022.24682.8938-2.0163.8441-0.1779-0.6091-0.21340.6715-0.1497-0.24160.080.35590.00760.2373-0.0763-0.02590.40190.0910.3497-35.043737.7827138.3646
210.73910.24760.490.97760.28090.58680.0611-0.1978-0.00140.1437-0.05530.1580.0893-0.133-0.0160.1095-0.01540.01190.1503-0.01540.0947-29.027241.889128.0694
221.2512-0.25850.12241.27490.63382.30860.0957-0.42940.5649-0.0185-0.16650.5035-0.3309-0.16670.03150.1613-0.02140.1120.3118-0.14250.2532-40.025353.5416133.383
231.79620.0210.42172.0633-0.19373.28340.0121-0.00810.2091-0.0336-0.02290.1564-0.3404-0.0060.00210.15980.02710.00770.1105-0.00180.1011-3.202215.500882.8875
240.954-0.00931.03781.2609-0.50921.19260.01670.26070.1017-0.2407-0.1013-0.11870.14980.2040.04530.21910.04450.00640.18460.03760.0917-3.27948.906568.1799
250.5376-0.76020.52941.832-0.4291.66020.11290.75460.0782-0.84680.13650.31460.4423-0.4683-0.17270.3584-0.0138-0.03690.49890.06420.22215.1185-2.212466.9215
261.3664-0.07340.61160.7773-0.50850.48770.09140.2433-0.0529-0.1959-0.0894-0.16630.14580.13090.01030.1690.03720.01660.1565-0.00790.12439.4633-4.191476.0814
270.7711-0.42490.39121.2565-0.34160.64550.09710.21810.0567-0.2289-0.0962-0.19660.0960.13690.01840.15730.02560.02240.15510.0070.08878.1306-3.352676.6349
281.1890.15910.24170.35380.33020.44440.2964-0.02560.63680.0385-0.49430.0985-0.39220.147-0.04770.5358-0.03930.20070.48410.04670.488310.977915.057174.2676
294.52670.0478-0.43951.88330.45891.85980.1770.48450.0719-0.3167-0.0630.6125-0.063-0.78630.02330.17730.0023-0.07080.35520.04380.2894-24.9512-16.7480.3528
300.4976-0.1766-0.56921.0532-0.29471.61390.0959-0.11280.05650.40220.05590.67090.0433-0.56530.13340.1941-0.03710.16890.28380.03690.3169-25.6352-17.206795.7036
310.59610.1368-0.08090.8028-0.3640.35240.0418-0.180.00250.35350.05360.17570.016-0.0166-0.08940.2397-0.02470.03320.16890.00640.1061-8.7723-19.388194.7725
320.74850.0638-0.43820.1185-0.15310.3624-0.26-0.15120.36210.20990.03350.2446-0.34940.32480.16730.4096-0.0117-0.10090.2603-0.03720.24440.1998-21.3311101.6068
331.2385-0.7214-0.28090.62560.06820.1026-0.1953-0.48780.28870.55830.14160.0422-0.20210.1431-0.10890.5263-0.005-0.06780.3506-0.03550.2005-2.8442-23.2798105.5845
342.91490.24120.83781.56850.01982.5233-0.0047-0.1924-0.06320.21430.04510.01520.1588-0.0325-0.01140.20870.00380.00450.09950.01750.0687-3.6674-30.476392.0893
352.7861-2.6847-0.21933.76-0.27590.7129-0.1338-0.25080.17750.15820.1702-0.3096-0.02750.05190.06740.15880.0023-0.02670.1274-0.03570.08736.069-24.847488.4321
361.22550.5449-0.38441.72290.01670.68690.1554-0.14790.04430.379-0.07670.1807-0.0707-0.0039-0.04730.2083-0.02060.03640.14510.00410.0977-11.6375-11.379293.5234
370.1402-0.0311-0.1490.1030.63934.3454-0.1403-0.1295-0.2840.47310.11830.13710.48830.2019-0.06530.3506-0.0205-0.00620.18640.06230.1577-8.1878-37.652397.1959
381.6894-0.6965-1.69052.378-0.71732.6507-0.23340.0659-0.07940.08620.07880.49520.5506-0.3905-0.08080.3959-0.09660.02990.26640.0570.159-17.3018-31.7187102.7469
390.85480.08050.04810.26730.4810.80210.60240.435-0.58-0.3334-0.208-0.50250.8760.6520.41170.49020.41920.05480.4619-0.17210.3267-66.8011-53.54474.1773
400.8906-0.10420.77561.15940.48730.91840.17530.5171-0.0439-0.3872-0.034-0.29540.03210.3507-0.07410.28320.08150.07270.29950.00350.2126-75.1475-38.399674.6118
411.4168-0.01770.22291.24560.57321.63970.19510.48560.3108-0.5938-0.2378-0.3392-0.11580.5001-0.04830.34290.0790.07780.40220.1180.2834-80.5787-30.695565.7385
421.2014-0.17970.4570.8697-0.01170.96480.24380.4069-0.0286-0.3214-0.1543-0.18330.21960.29-0.06090.27630.09790.03070.2527-0.010.1299-78.779-39.355373.8824
430.9122-0.30040.56921.5781-0.17871.7270.0105-0.02750.13280.2887-0.1459-0.6985-0.19090.399-0.0250.1814-0.0498-0.08690.21860.07660.4569-53.3684-30.1777103.5994
440.6137-0.1458-0.23170.29440.04320.11530.1071-0.3228-0.3940.52760.0634-0.20880.8712-0.0628-0.0470.5441-0.046-0.08930.21980.07820.2987-72.519-31.61109.1445
451.1265-0.48040.33932.3637-0.00130.53470.09760.08010.1139-0.0056-0.1442-0.28310.02050.05240.06650.0931-0.0123-0.00630.11480.03210.1788-69.2873-26.196495.5313
461.21860.33750.40484.6508-0.35590.7014-0.0078-0.2646-0.39790.429-0.07070.26820.4709-0.2790.00020.3619-0.10290.06540.25930.03630.352-81.0683-28.1841107.9305
470.9025-0.62330.27951.7745-0.15490.28820.0531-0.0345-0.02630.0531-0.0443-0.10910.0127-0.0142-0.00870.1231-0.0167-0.0080.11740.03490.1558-72.2517-28.128498.2037
481.25230.9938-0.21423.5007-1.24282.5248-0.0535-0.1560.12390.447-0.1438-0.5064-0.0860.14970.17520.2434-0.0279-0.05610.1736-0.01420.2336-68.5011-15.3758110.8031
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 115 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 116 through 315 )A0
3X-RAY DIFFRACTION3chain 'B' and (resid 3 through 30 )B0
4X-RAY DIFFRACTION4chain 'B' and (resid 31 through 85 )B0
5X-RAY DIFFRACTION5chain 'B' and (resid 86 through 153 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 154 through 199 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 200 through 221 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 222 through 315 )B0
9X-RAY DIFFRACTION9chain 'C' and (resid 3 through 30 )C0
10X-RAY DIFFRACTION10chain 'C' and (resid 31 through 53 )C0
11X-RAY DIFFRACTION11chain 'C' and (resid 54 through 85 )C0
12X-RAY DIFFRACTION12chain 'C' and (resid 86 through 153 )C0
13X-RAY DIFFRACTION13chain 'C' and (resid 154 through 174 )C0
14X-RAY DIFFRACTION14chain 'C' and (resid 175 through 199 )C0
15X-RAY DIFFRACTION15chain 'C' and (resid 200 through 280 )C0
16X-RAY DIFFRACTION16chain 'C' and (resid 281 through 312 )C0
17X-RAY DIFFRACTION17chain 'D' and (resid 1 through 30 )D0
18X-RAY DIFFRACTION18chain 'D' and (resid 31 through 85 )D0
19X-RAY DIFFRACTION19chain 'D' and (resid 86 through 153 )D0
20X-RAY DIFFRACTION20chain 'D' and (resid 154 through 185 )D0
21X-RAY DIFFRACTION21chain 'D' and (resid 186 through 280 )D0
22X-RAY DIFFRACTION22chain 'D' and (resid 281 through 315 )D0
23X-RAY DIFFRACTION23chain 'E' and (resid 1 through 53 )E0
24X-RAY DIFFRACTION24chain 'E' and (resid 54 through 85 )E0
25X-RAY DIFFRACTION25chain 'E' and (resid 86 through 115 )E0
26X-RAY DIFFRACTION26chain 'E' and (resid 116 through 199 )E0
27X-RAY DIFFRACTION27chain 'E' and (resid 200 through 302 )E0
28X-RAY DIFFRACTION28chain 'E' and (resid 303 through 316 )E0
29X-RAY DIFFRACTION29chain 'F' and (resid 3 through 30 )F0
30X-RAY DIFFRACTION30chain 'F' and (resid 31 through 85 )F0
31X-RAY DIFFRACTION31chain 'F' and (resid 86 through 153 )F0
32X-RAY DIFFRACTION32chain 'F' and (resid 154 through 174 )F0
33X-RAY DIFFRACTION33chain 'F' and (resid 175 through 199 )F0
34X-RAY DIFFRACTION34chain 'F' and (resid 200 through 221 )F0
35X-RAY DIFFRACTION35chain 'F' and (resid 222 through 237 )F0
36X-RAY DIFFRACTION36chain 'F' and (resid 238 through 280 )F0
37X-RAY DIFFRACTION37chain 'F' and (resid 281 through 297 )F0
38X-RAY DIFFRACTION38chain 'F' and (resid 298 through 312 )F0
39X-RAY DIFFRACTION39chain 'G' and (resid 3 through 85 )G0
40X-RAY DIFFRACTION40chain 'G' and (resid 86 through 153 )G0
41X-RAY DIFFRACTION41chain 'G' and (resid 154 through 199 )G0
42X-RAY DIFFRACTION42chain 'G' and (resid 200 through 316 )G0
43X-RAY DIFFRACTION43chain 'H' and (resid 3 through 85 )H0
44X-RAY DIFFRACTION44chain 'H' and (resid 86 through 115 )H0
45X-RAY DIFFRACTION45chain 'H' and (resid 116 through 153 )H0
46X-RAY DIFFRACTION46chain 'H' and (resid 154 through 199 )H0
47X-RAY DIFFRACTION47chain 'H' and (resid 200 through 280 )H0
48X-RAY DIFFRACTION48chain 'H' and (resid 281 through 315 )H0

+
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