[English] 日本語
Yorodumi
- PDB-6qne: Y102G mutated sulfur oxygenase reductase from Acidianus ambivalens -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6qne
TitleY102G mutated sulfur oxygenase reductase from Acidianus ambivalens
ComponentsSulfur oxygenase/reductase
KeywordsOXIDOREDUCTASE / SULFUR OXYGENASE REDUCTASE / 2-HIS-1-CARBOXYLATE FACIAL TRIAD / CYSTEINE PERSULPHURATION / BIOGEOCHEMICAL SULFUR CYCLE
Function / homologysulfur oxygenase/reductase / sulfur oxygenase/reductase activity / Sulphur oxygenase reductase / Sulphur oxygenase reductase / Dimeric alpha-beta barrel / metal ion binding / cytoplasm / : / Sulfur oxygenase/reductase
Function and homology information
Biological speciesAcidianus ambivalens (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsFrazao, C. / Klezin, A. / Poell, U.
Funding support Portugal, Germany, 2items
OrganizationGrant numberCountry
Foundation for Science and TechnologyLIOA-01-0145-FEDER-007660 Portugal
German Research FoundationKl885-7/1 Germany
Citation
Journal: To Be Published
Title: Multiple sulfane modifications in active-site cysteine thiols of two sulfur oxygenase reductases and analysis of substrate/product channels
Authors: Frazao, C. / Klezin, A.
#1: Journal: Science / Year: 2006
Title: X-ray Structure of a self-compartmentalizing sulfur cycle metalloenzyme.
Authors: Urich, T. / Gomes, C.M. / Kletzin, A. / Frazao, C.
#2: Journal: Front Microbiol / Year: 2011
Title: Substrate pathways and mechanisms of inhibition in the sulfur oxygenase reductase of acidianus ambivalens.
Authors: Veith, A. / Urich, T. / Seyfarth, K. / Protze, J. / Frazao, C. / Kletzin, A.
History
DepositionFeb 11, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 4, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: 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: Sulfur oxygenase/reductase
B: Sulfur oxygenase/reductase
C: Sulfur oxygenase/reductase
D: Sulfur oxygenase/reductase
E: Sulfur oxygenase/reductase
F: Sulfur oxygenase/reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)217,98412
Polymers217,6496
Non-polymers3356
Water13,205733
1
A: Sulfur oxygenase/reductase
C: Sulfur oxygenase/reductase
D: Sulfur oxygenase/reductase
hetero molecules

A: Sulfur oxygenase/reductase
C: Sulfur oxygenase/reductase
D: Sulfur oxygenase/reductase
hetero molecules

A: Sulfur oxygenase/reductase
C: Sulfur oxygenase/reductase
D: Sulfur oxygenase/reductase
hetero molecules

A: Sulfur oxygenase/reductase
C: Sulfur oxygenase/reductase
D: Sulfur oxygenase/reductase
hetero molecules

B: Sulfur oxygenase/reductase
E: Sulfur oxygenase/reductase
F: Sulfur oxygenase/reductase
hetero molecules

B: Sulfur oxygenase/reductase
E: Sulfur oxygenase/reductase
F: Sulfur oxygenase/reductase
hetero molecules

B: Sulfur oxygenase/reductase
E: Sulfur oxygenase/reductase
F: Sulfur oxygenase/reductase
hetero molecules

B: Sulfur oxygenase/reductase
E: Sulfur oxygenase/reductase
F: Sulfur oxygenase/reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)871,93648
Polymers870,59624
Non-polymers1,34024
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,-y,z1
crystal symmetry operation3_645-y+1,x-1,z1
crystal symmetry operation4_665y+1,-x+1,z1
crystal symmetry operation5_545x+1/2,y-1/2,z+1/21
crystal symmetry operation6_655-x+3/2,-y+1/2,z+1/21
crystal symmetry operation7_645-y+3/2,x-1/2,z+1/21
crystal symmetry operation8_555y+1/2,-x+1/2,z+1/21
Buried area135480 Å2
ΔGint-1138 kcal/mol
Surface area213420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)161.321, 161.321, 154.004
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

-
Components

#1: Protein
Sulfur oxygenase/reductase / / Sulfur oxygenase reductase / SOR


Mass: 36274.816 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acidianus ambivalens (archaea) / Gene: sor / Production host: Escherichia coli (E. coli) / References: UniProt: P29082, sulfur oxygenase/reductase
#2: Chemical
ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 733 / 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: 2.3 Å3/Da / Density % sol: 46.41 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6 / Details: 0.1 M sodium acetate pH 4.6, 2 M sodium formate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97242 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 9, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97242 Å / Relative weight: 1
ReflectionResolution: 1.8→65.33 Å / Num. obs: 179725 / % possible obs: 99.9 % / Redundancy: 3.87 % / Biso Wilson estimate: 32 Å2 / CC1/2: 0.998 / Rpim(I) all: 0.008 / Rrim(I) all: 0.0246 / Rsym value: 0.0228 / Net I/σ(I): 11.58
Reflection shellResolution: 1.8→1.89 Å / Redundancy: 3.97 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 29116 / CC1/2: 0.564 / Rpim(I) all: 0.028 / Rrim(I) all: 0.985 / Rsym value: 0.092 / % possible all: 99.1

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6QMV
Resolution: 1.8→65.33 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.89 / Phase error: 22.9
RfactorNum. reflection% reflection
Rfree0.2058 5877 1.7 %
Rwork0.1656 --
obs0.1663 179725 95.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.8→65.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14748 0 6 733 15487
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01415576
X-RAY DIFFRACTIONf_angle_d1.04621025
X-RAY DIFFRACTIONf_dihedral_angle_d13.8555911
X-RAY DIFFRACTIONf_chiral_restr0.0432172
X-RAY DIFFRACTIONf_plane_restr0.0052718
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7986-1.8190.36542050.354811088X-RAY DIFFRACTION94
1.819-1.84040.34131760.322511614X-RAY DIFFRACTION97
1.8404-1.86280.31670.305311362X-RAY DIFFRACTION96
1.8628-1.88640.32871840.291211350X-RAY DIFFRACTION96
1.8864-1.91130.30911960.305211386X-RAY DIFFRACTION96
1.9113-1.93740.38572080.320211156X-RAY DIFFRACTION95
1.9374-1.96510.30331990.267711391X-RAY DIFFRACTION96
1.9651-1.99450.3111770.249311343X-RAY DIFFRACTION96
1.9945-2.02560.27642350.242511290X-RAY DIFFRACTION96
2.0256-2.05880.30531680.231911181X-RAY DIFFRACTION95
2.0588-2.09430.25162160.215511335X-RAY DIFFRACTION96
2.0943-2.13240.24911890.202611544X-RAY DIFFRACTION98
2.1324-2.17340.21511720.189411495X-RAY DIFFRACTION97
2.1734-2.21780.21362160.18511535X-RAY DIFFRACTION97
2.2178-2.2660.24881920.201711137X-RAY DIFFRACTION95
2.266-2.31870.25461690.171311483X-RAY DIFFRACTION97
2.3187-2.37670.21062170.164411468X-RAY DIFFRACTION97
2.3767-2.4410.20612010.166311276X-RAY DIFFRACTION96
2.441-2.51280.19532240.164511190X-RAY DIFFRACTION95
2.5128-2.59390.22032100.161811550X-RAY DIFFRACTION98
2.5939-2.68670.21812140.167211425X-RAY DIFFRACTION97
2.6867-2.79420.22021750.162811354X-RAY DIFFRACTION97
2.7942-2.92140.19422230.150511364X-RAY DIFFRACTION96
2.9214-3.07540.19732350.154211302X-RAY DIFFRACTION96
3.0754-3.26810.19831850.151310979X-RAY DIFFRACTION93
3.2681-3.52040.17171810.138411312X-RAY DIFFRACTION96
3.5204-3.87460.17921890.133511154X-RAY DIFFRACTION94
3.8746-4.43520.14661870.119710768X-RAY DIFFRACTION91
4.4352-5.58740.14471930.119810966X-RAY DIFFRACTION93
5.5874-65.37460.1991740.149311151X-RAY DIFFRACTION94
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)
10.73490.2580.44120.28220.13880.20920.2299-0.0607-0.1282-0.02320.16350.1157-0.0326-0.44810.00080.2498-0.0174-0.00210.25210.06660.2653156.468328.390639.0582
20.41720.22190.12320.11460.00490.03610.0613-0.02170.1454-0.06810.00710.0812-0.0514-0.180300.23260.0047-0.01720.2547-0.00270.2221149.185326.917833.9997
30.0713-0.0204-0.14210.30820.10130.3567-0.0203-0.1484-0.11210.07550.098-0.15450.25380.11870.00010.2999-0.0081-0.0040.27860.0210.2974171.816622.328244.2062
40.12710.22820.01510.3329-0.0004-0.0306-0.03270.11410.1516-0.0146-0.02640.0882-0.10670.0963-00.3037-0.0019-0.00620.26590.03410.2565152.874134.713626.8068
5-0.017-0.0040.00560.1153-0.13160.0680.0551-0.01670.3074-0.0198-0.2358-0.57250.0649-0.0273-0.00040.4867-0.0091-0.00070.4006-0.01440.4189143.448737.654236.6861
60.1789-0.09380.27030.32910.33160.3682-0.0593-0.0674-0.0593-0.0198-0.12770.062-0.1084-0.1525-00.2407-0.01940.00030.27870.01660.2455159.579433.60334.3415
70.31980.04720.18530.34560.14810.11870.00320.10670.0638-0.131-0.09440.1833-0.0336-0.0646-00.25360.0205-0.00020.26160.00990.2019157.35919.456915.4598
80.23730.39170.08560.0319-0.27470.6052-0.00040.0801-0.0189-0.0578-0.02690.0323-0.0840.08870.00010.2147-0.01680.02740.22520.01850.1888170.385226.19924.0511
90.31820.09860.0890.1970.22710.147-0.07060.107-0.06070.0749-0.11050.171-0.0112-0.2297-0.00030.32890.01030.02440.30710.01790.2959149.57446.334339.8895
100.50450.14520.21170.7395-0.110.44460.02580.1091-0.031-0.0209-0.0139-0.1084-0.05030.1339-00.2583-0.02120.02320.25710.00840.222176.128126.937427.4231
110.31-0.09650.14290.35170.19860.20290.03160.04320.00630.0156-0.04630.0982-0.1246-0.072200.2118-0.01790.00030.2381-0.00540.2013159.023222.816127.9849
120.37070.3685-0.22280.2920.01420.7546-0.17670.18070.4251-0.17380.1643-0.0418-0.0065-0.033200.2532-0.0474-0.02860.26580.04210.254121.321283.617328.7649
130.0082-0.09280.04070.4471-0.27040.0566-0.0558-0.16450.05360.01310.0335-0.0702-0.07460.039100.2452-0.03070.00340.2586-0.04090.2594128.83788.62626.2561
140.21820.06960.09620.06640.15720.33130.02330.1869-0.0964-0.3522-0.0047-0.10420.219-0.0613-0.00010.30130.00710.01990.305-0.00660.2932114.263668.986126.118
150.20680.095-0.1750.1117-0.18450.15180.13130.00350.13690.0133-0.0942-0.0294-0.28530.010400.2934-0.03860.0020.2976-0.04780.3066133.261190.560435.8896
160.0650.0368-0.00610.0201-0.00530.023-0.1909-0.09920.00970.5251-0.19860.50460.1921-0.16770.00190.3589-0.03660.08410.4554-0.02630.3993119.677895.777632.467
170.38470.1692-0.38930.04580.01240.35020.1049-0.10310.0187-0.07130.0581-0.01710.0131-0.01540.00010.2111-0.0091-0.00110.2488-0.00770.2611128.767878.749731.5326
180.1950.0963-0.20160.2048-0.08410.17520.2461-0.5524-0.19930.2476-0.0550.0489-0.19450.38160.00030.2326-0.0199-0.01590.3804-0.02680.3224145.771174.02698.8348
190.28160.1820.13590.2112-0.4550.09370.0087-0.0192-0.0132-0.00030.0529-0.0916-0.09110.058400.17980.0278-0.01740.204-0.0190.2083133.967366.003828.2518
200.5129-0.0671-0.07730.2809-0.1190.56380.0991-0.00670.1577-0.09750.02-0.0481-0.18540.0050.00010.2894-0.0148-0.0070.2742-0.01980.2995124.088191.00945.165
210.4725-0.055-0.24850.14810.30550.3405-0.055-0.0134-0.08540.02070.057-0.0650.03970.018200.21280.0069-0.00840.2151-0.00970.2175128.292662.828229.7479
220.01530.0355-0.05990.108-0.15030.114-0.30280.11550.09-0.09380.2448-0.099-0.29230.0572-0.00050.2256-0.02270.0020.2246-0.03610.3243138.956581.456722.6314
230.58140.034-0.5910.1557-0.17430.41230.0005-0.0125-0.0488-0.4051-0.1695-0.15330.13050.2288-00.30270.07590.04430.27160.05290.3086142.354644.489668.8502
240.21880.1330.06440.23420.26070.2573-0.07590.1165-0.0198-0.19950.05070.20920.154-0.093-0.00010.3137-0.00640.01690.27980.01810.2675145.742749.102761.4968
250.26460.30310.17110.31630.14550.10320.0663-0.1584-0.0470.0108-0.0033-0.268-0.10050.174900.25390.03250.00520.23170.02110.2673144.371739.168783.9834
260.45790.0468-0.2959-0.0307-0.02410.1564-0.01070.35370.0565-0.09420.02690.0868-0.2529-0.3333-00.32870.01360.01690.32830.04950.323137.212655.288759.5125
270.0285-0.0384-0.03080.02150.02080.0265-0.0777-0.5626-0.16780.1704-0.24140.0789-0.08270.07770.00080.5124-0.09210.04730.56680.08890.433137.76440.026757.3131
280.42390.29070.40450.12970.03930.1231-0.01720.1472-0.0392-0.04160.0949-0.0611-0.01480.0350.00010.27850.01060.02910.24250.02090.2744143.400752.757872.2204
290.6497-0.07020.09090.02310.0030.075-0.12160.39620.2493-0.37190.25590.5815-0.20540.0940.03620.3160.0168-0.01330.14690.05710.3364166.557566.785873.6577
300.1249-0.2284-0.09540.03980.04360.17120.0110.04180.037-0.0428-0.01260.036-0.17880.034-00.2490.03360.01360.19110.00760.2526144.897759.02783.2969
310.56730.11510.07530.25520.23990.1148-0.08660.1717-0.0171-0.310.0769-0.0604-0.0249-0.0089-0.00020.30610.03480.01520.27360.03430.2624126.044847.336359.83
320.3144-0.40280.31620.4295-0.54580.24840.0467-0.04720.02940.0273-0.01330.0106-0.1630.0138-00.22430.02280.02170.2263-0.00770.2672142.800456.000789.3556
330.32250.35660.22070.23620.24220.262-0.04780.0736-0.1190.0446-0.0101-0.0855-0.2659-0.0061-0.00010.23530.02080.02950.23930.0120.2746149.53254.412271.956
340.57670.1440.31610.12430.0360.2440.1259-0.2731-0.1338-0.0465-0.1769-0.39860.08930.010900.2492-0.03770.0010.28630.07080.2609179.023436.945952.3511
350.3404-0.08760.29450.0648-0.10180.07970.1389-0.0075-0.1504-0.0479-0.04560.0326-0.14390.242300.2478-0.02310.01810.2885-0.00020.2946187.834642.388154.5736
360.1855-0.0086-0.14660.41710.2630.2972-0.0635-0.1240.11730.29350.00920.10960.0526-0.2127-00.3378-0.0090.02010.26880.00310.2824162.153635.58855.2017
370.1102-0.0987-0.01530.22130.16190.1016-0.02260.11640.0257-0.13670.0387-0.14140.07640.221800.3084-0.03710.02870.32520.00370.3067189.082244.188145.5077
380.04020.05310.01010.02080.00490.00320.24090.3655-0.19120.08050.18570.11940.1905-0.611-0.00040.43850.0261-0.09690.5817-0.04460.4823186.394929.215549.1969
390.43560.16960.09590.18610.3640.4018-0.07680.0009-0.00320.00560.140.0919-0.04190.043500.2666-0.03230.01870.22870.03290.2543176.601846.469948.7354
400.126-0.03110.00080.18250.12770.0862-0.08440.09910.0669-0.10310.1415-0.1417-0.20640.53490.00090.3366-0.07980.02810.29290.01380.3406178.68662.564271.8254
410.1116-0.02550.45590.0916-0.45680.207-0.0168-0.0620.1025-0.0760.0252-0.05530.0140.0857-00.2711-0.00250.02940.19970.01650.2074167.192654.847751.8313
42-0.07080.14310.13770.52610.47180.29360.0316-0.0444-0.08320.0030.1558-0.09330.08590.0967-00.28090.00620.01750.25250.00550.2526187.462435.626535.5765
430.11340.0845-0.4340.0124-0.03220.39610.01170.0130.0553-0.0498-0.02710.0111-0.0504-0.0097-00.26280.00270.00940.22540.01470.2513160.595752.698950.3027
440.3528-0.2225-0.14850.22430.25990.27020.04170.00270.070.04670.0014-0.08770.02810.021200.25-0.0179-0.00030.24380.03140.2176177.711849.014457.2867
450.13080.08690.21850.39260.19310.2739-0.1091-0.26820.2095-0.09330.030.002-0.1502-0.0215-0.00020.29950.0665-0.04860.2324-0.05730.2931114.836346.815711.8464
460.0164-0.2216-0.10430.21190.16460.2779-0.0236-0.1251-0.10950.0840.04460.06070.038-0.1857-0.00010.29570.0322-0.00280.2956-0.01650.2648120.187348.668718.3914
470.2505-0.0664-0.06430.103-0.1830.14070.05810.06320.1478-0.19020.0314-0.0817-0.11040.198-00.28740.02770.00160.2847-0.01740.3051110.732250.4264-3.416
480.42160.2329-0.11730.12530.10440.25540.1547-0.2234-0.05830.1683-0.10470.11390.00520.1139-00.28420.0274-0.0170.25210.01890.2733123.086238.006621.6365
490.01970.00860.01990.05310.03510.0232-0.0689-0.25940.0575-0.17980.2433-0.12360.2419-0.22520.00030.44620.004-0.11290.36810.01520.4173109.111744.304223.4818
500.22170.17380.24690.2035-0.19990.17840.1637-0.1963-0.0125-0.0125-0.14420.0062-0.00950.0591-00.22830.03830.00070.2378-0.04060.2472122.371942.86128.7834
510.25710.24140.14230.50460.09450.13590.1608-0.3901-0.5570.4127-0.27750.04570.0935-0.04550.00540.19350.0435-0.02590.27870.01610.3305143.435761.82977.5481
520.3915-0.2074-0.03340.10790.05650.06010.01370.0345-0.07160.0919-0.0453-0.0132-0.00250.0903-00.19450.03590.02110.1772-0.02640.1943129.759644.119-2.1794
530.47790.3324-0.0930.23850.06580.08680.031-0.1910.09660.0813-0.0133-0.04910.01030.11970.00010.26320.019-0.02240.2423-0.01060.2713111.695430.690121.1599
540.33760.09940.14770.6328-0.30380.1508-0.01560.1208-0.0485-0.08350.0136-0.02260.02750.164100.23910.03030.01380.2418-0.03860.2345126.030143.0024-8.3747
550.1970.2404-0.08050.16830.120.38950.02220.07160.0132-0.017-0.0504-0.05550.09370.2368-0.00040.23630.03390.00830.2215-0.02360.2533126.851549.93849.0546
560.6232-0.0078-0.35710.2742-0.20370.27550.14560.0950.0851-0.0630.16740.16090.3476-0.32590.00030.2634-0.0336-0.04270.29490.05470.297105.281265.929141.9671
570.20430.40370.00230.49830.16480.0918-0.005-0.006-0.0531-0.14650.01090.06920.15630.0839-00.26920.01250.01090.23780.01710.254101.353259.98646.8845
580.2127-0.1766-0.20490.3781-0.01450.45960.01910.01340.17310.021-0.01670.1121-0.282-0.1536-00.3185-0.00640.01060.2893-0.01630.2874105.352381.39337.2371
590.44320.3774-0.14130.2705-0.10830.00340.02-0.0171-0.25370.1191-0.1017-0.05470.1279-0.06870.00010.26980.0324-0.00140.28310.02550.2704110.291955.206651.7211
600.10780.04390.07070.01980.00910.0461-0.0206-0.190.0547-0.28420.4941-0.17980.12050.19660.00010.4996-0.02020.10660.5109-0.08130.4506106.533254.445635.9106
610.5313-0.4722-0.5737-0.26120.07250.1146-0.13740.0757-0.110.02970.01660.04180.0899-0.0064-00.2726-0.00840.00690.24720.00110.2518101.618570.002153.3791
620.1136-0.01470.01440.014-0.03260.1144-0.0723-0.3221-0.07610.2979-0.0015-0.2119-0.00080.3437-0.00020.3180.0224-0.00520.34430.01820.231888.760574.812570.1523
630.2030.31320.07110.1883-0.12820.3158-0.10380.1082-0.02590.09080.09350.0036-0.01870.099100.20260.0032-0.01990.2027-0.01440.1956108.222580.529156.9819
640.6245-0.1974-0.26240.19370.44660.2693-0.09740.0014-0.20020.01810.08150.0060.0832-0.01460.00010.27260.0079-0.00130.2621-0.00770.2656119.453255.100543.0265
650.496-0.24740.0560.2972-0.05880.24190.028-0.03430.06090.06110.0065-0.0169-0.0520.0469-00.2263-0.0109-0.00910.227-0.00640.2128110.673285.562753.7021
660.1172-0.1386-0.08320.1665-0.03790.1485-0.05210.0633-0.02240.15040.08920.01330.0053-0.11750.00010.1778-0.00170.00160.2025-0.00420.1677101.122770.296853.0589
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 2:21)
2X-RAY DIFFRACTION2(chain A and resid 22:49)
3X-RAY DIFFRACTION3(chain A and resid 50:73)
4X-RAY DIFFRACTION4(chain A and resid 74:88)
5X-RAY DIFFRACTION5(chain A and resid 89:103)
6X-RAY DIFFRACTION6(chain A and resid 104:123)
7X-RAY DIFFRACTION7(chain A and resid 124:150)
8X-RAY DIFFRACTION8(chain A and resid 151:202)
9X-RAY DIFFRACTION9(chain A and resid 203:239)
10X-RAY DIFFRACTION10(chain A and resid 240:287)
11X-RAY DIFFRACTION11(chain A and resid 288:308)
12X-RAY DIFFRACTION12(chain B and resid 2:22)
13X-RAY DIFFRACTION13(chain B and resid 23:49)
14X-RAY DIFFRACTION14(chain B and resid 50:75)
15X-RAY DIFFRACTION15(chain B and resid 76:98)
16X-RAY DIFFRACTION16(chain B and resid 99:104)
17X-RAY DIFFRACTION17(chain B and resid 105:128)
18X-RAY DIFFRACTION18(chain B and resid 129:149)
19X-RAY DIFFRACTION19(chain B and resid 150:199)
20X-RAY DIFFRACTION20(chain B and resid 200:241)
21X-RAY DIFFRACTION21(chain B and resid 242:296)
22X-RAY DIFFRACTION22(chain B and resid 297:308)
23X-RAY DIFFRACTION23(chain C and resid 2:21)
24X-RAY DIFFRACTION24(chain C and resid 22:48)
25X-RAY DIFFRACTION25(chain C and resid 49:75)
26X-RAY DIFFRACTION26(chain C and resid 76:98)
27X-RAY DIFFRACTION27(chain C and resid 99:105)
28X-RAY DIFFRACTION28(chain C and resid 106:130)
29X-RAY DIFFRACTION29(chain C and resid 131:150)
30X-RAY DIFFRACTION30(chain C and resid 151:201)
31X-RAY DIFFRACTION31(chain C and resid 202:241)
32X-RAY DIFFRACTION32(chain C and resid 242:288)
33X-RAY DIFFRACTION33(chain C and resid 289:308)
34X-RAY DIFFRACTION34(chain D and resid 2:22)
35X-RAY DIFFRACTION35(chain D and resid 23:47)
36X-RAY DIFFRACTION36(chain D and resid 48:73)
37X-RAY DIFFRACTION37(chain D and resid 74:99)
38X-RAY DIFFRACTION38(chain D and resid 100:106)
39X-RAY DIFFRACTION39(chain D and resid 107:127)
40X-RAY DIFFRACTION40(chain D and resid 128:150)
41X-RAY DIFFRACTION41(chain D and resid 151:201)
42X-RAY DIFFRACTION42(chain D and resid 202:241)
43X-RAY DIFFRACTION43(chain D and resid 242:288)
44X-RAY DIFFRACTION44(chain D and resid 289:308)
45X-RAY DIFFRACTION45(chain E and resid 2:21)
46X-RAY DIFFRACTION46(chain E and resid 22:50)
47X-RAY DIFFRACTION47(chain E and resid 51:75)
48X-RAY DIFFRACTION48(chain E and resid 76:98)
49X-RAY DIFFRACTION49(chain E and resid 99:105)
50X-RAY DIFFRACTION50(chain E and resid 106:128)
51X-RAY DIFFRACTION51(chain E and resid 129:149)
52X-RAY DIFFRACTION52(chain E and resid 150:201)
53X-RAY DIFFRACTION53(chain E and resid 202:241)
54X-RAY DIFFRACTION54(chain E and resid 242:288)
55X-RAY DIFFRACTION55(chain E and resid 289:308)
56X-RAY DIFFRACTION56(chain F and resid 2:21)
57X-RAY DIFFRACTION57(chain F and resid 22:50)
58X-RAY DIFFRACTION58(chain F and resid 51:75)
59X-RAY DIFFRACTION59(chain F and resid 76:98)
60X-RAY DIFFRACTION60(chain F and resid 99:106)
61X-RAY DIFFRACTION61(chain F and resid 107:137)
62X-RAY DIFFRACTION62(chain F and resid 138:152)
63X-RAY DIFFRACTION63(chain F and resid 153:198)
64X-RAY DIFFRACTION64(chain F and resid 199:241)
65X-RAY DIFFRACTION65(chain F and resid 242:287)
66X-RAY DIFFRACTION66(chain F and resid 288:308)

+
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