[English] 日本語
Yorodumi
- PDB-6fah: Molecular basis of the flavin-based electron-bifurcating caffeyl-... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6fah
TitleMolecular basis of the flavin-based electron-bifurcating caffeyl-CoA reductase reaction
Components(Caffeyl-CoA reductase-Etf complex subunit ...) x 3
KeywordsFLAVOPROTEIN / Acetogenic bacteria / bioenergetics / flavin-based electron bifurcation / electron-transfer protein/acyl-CoA dehydrogenase / ferredoxin
Function / homology
Function and homology information


caffeoyl-CoA reductase / oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor / acyl-CoA dehydrogenase activity / FAD binding / 4 iron, 4 sulfur cluster binding / electron transfer activity / metal ion binding / cytoplasm
Similarity search - Function
Electron transfer flavoprotein, beta-subunit, conserved site / Electron transfer flavoprotein beta-subunit signature. / Electron transfer flavoprotein, beta subunit / Electron transfer flavoprotein, alpha subunit, N-terminal / Electron transfer flavoprotein, beta subunit, N-terminal / Electron transfer flavoprotein alpha subunit/FixB / Electron transfer flavoprotein domain / Electron transfer flavoprotein, alpha/beta-subunit, N-terminal / Electron transfer flavoprotein, alpha subunit, C-terminal / Electron transfer flavoprotein FAD-binding domain ...Electron transfer flavoprotein, beta-subunit, conserved site / Electron transfer flavoprotein beta-subunit signature. / Electron transfer flavoprotein, beta subunit / Electron transfer flavoprotein, alpha subunit, N-terminal / Electron transfer flavoprotein, beta subunit, N-terminal / Electron transfer flavoprotein alpha subunit/FixB / Electron transfer flavoprotein domain / Electron transfer flavoprotein, alpha/beta-subunit, N-terminal / Electron transfer flavoprotein, alpha subunit, C-terminal / Electron transfer flavoprotein FAD-binding domain / Electron transfer flavoprotein domain / 4Fe-4S dicluster domain / Acyl-CoA dehydrogenases signature 1. / Acyl-CoA dehydrogenases signature 2. / Acyl-CoA dehydrogenase, conserved site / Butyryl-Coa Dehydrogenase, subunit A; domain 1 / Acyl-CoA dehydrogenase/oxidase, N-terminal domain / Butyryl-CoA Dehydrogenase, subunit A, domain 2 / Butyryl-CoA Dehydrogenase, subunit A; domain 2 / Acyl-CoA dehydrogenase/oxidase C-terminal / Acyl-CoA dehydrogenase/oxidase, N-terminal / Acyl-CoA dehydrogenase, C-terminal domain / Acyl-CoA dehydrogenase, N-terminal domain / Acyl-CoA oxidase/dehydrogenase, middle domain / Acyl-CoA dehydrogenase, middle domain / Acyl-CoA dehydrogenase/oxidase, N-terminal domain superfamily / Butyryl-CoA Dehydrogenase, subunit A, domain 3 / Acyl-CoA dehydrogenase/oxidase, N-terminal and middle domain superfamily / Acyl-CoA dehydrogenase-like, C-terminal / Butyryl-CoA Dehydrogenase, subunit A; domain 3 / DHS-like NAD/FAD-binding domain superfamily / HUPs / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / Rossmann-like alpha/beta/alpha sandwich fold / Up-down Bundle / Beta Barrel / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / IRON/SULFUR CLUSTER / Caffeyl-CoA reductase-Etf complex subunit CarC / Caffeyl-CoA reductase-Etf complex subunit CarD / Caffeyl-CoA reductase-Etf complex subunit CarE
Similarity search - Component
Biological speciesAcetobacterium woodii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.133 Å
AuthorsDemmer, J.K. / Bertsch, J. / Oeppinger, C. / Wohlers, H. / Kayastha, K. / Demmer, U. / Ermler, U. / Mueller, V.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation Germany
CitationJournal: FEBS Lett. / Year: 2018
Title: Molecular basis of the flavin-based electron-bifurcating caffeyl-CoA reductase reaction.
Authors: Demmer, J.K. / Bertsch, J. / Oppinger, C. / Wohlers, H. / Kayastha, K. / Demmer, U. / Ermler, U. / Muller, V.
History
DepositionDec 15, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 24, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 21, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 17, 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 / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn_type.id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Caffeyl-CoA reductase-Etf complex subunit CarE
B: Caffeyl-CoA reductase-Etf complex subunit CarD
C: Caffeyl-CoA reductase-Etf complex subunit CarC
D: Caffeyl-CoA reductase-Etf complex subunit CarC
E: Caffeyl-CoA reductase-Etf complex subunit CarE
F: Caffeyl-CoA reductase-Etf complex subunit CarD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)231,36123
Polymers224,5696
Non-polymers6,79217
Water00
1
A: Caffeyl-CoA reductase-Etf complex subunit CarE
B: Caffeyl-CoA reductase-Etf complex subunit CarD
C: Caffeyl-CoA reductase-Etf complex subunit CarC
D: Caffeyl-CoA reductase-Etf complex subunit CarC
E: Caffeyl-CoA reductase-Etf complex subunit CarE
F: Caffeyl-CoA reductase-Etf complex subunit CarD
hetero molecules

A: Caffeyl-CoA reductase-Etf complex subunit CarE
B: Caffeyl-CoA reductase-Etf complex subunit CarD
C: Caffeyl-CoA reductase-Etf complex subunit CarC
D: Caffeyl-CoA reductase-Etf complex subunit CarC
E: Caffeyl-CoA reductase-Etf complex subunit CarE
F: Caffeyl-CoA reductase-Etf complex subunit CarD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)462,72246
Polymers449,13712
Non-polymers13,58534
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area79260 Å2
ΔGint-821 kcal/mol
Surface area165410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)213.740, 144.260, 102.840
Angle α, β, γ (deg.)90.00, 98.93, 90.00
Int Tables number5
Space group name H-MC121

-
Components

-
Caffeyl-CoA reductase-Etf complex subunit ... , 3 types, 6 molecules AEBFCD

#1: Protein Caffeyl-CoA reductase-Etf complex subunit CarE / Electron transfer flavoprotein large subunit / ETFLS / Electron transfer flavoprotein subunit alpha ...Electron transfer flavoprotein large subunit / ETFLS / Electron transfer flavoprotein subunit alpha / Alpha-ETF


Mass: 42530.805 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: 1 FAD; 2 Fe-S clusters
Source: (natural) Acetobacterium woodii (strain ATCC 29683 / DSM 1030 / JCM 2381 / KCTC 1655 / WB1) (bacteria)
Strain: ATCC 29683 / DSM 1030 / JCM 2381 / KCTC 1655 / WB1 / References: UniProt: H6LGM8, caffeoyl-CoA reductase
#2: Protein Caffeyl-CoA reductase-Etf complex subunit CarD / Electron transfer flavoprotein small subunit / ETFSS / Electron transfer flavoprotein subunit beta / Beta-ETF


Mass: 28265.518 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: 1 FAD
Source: (natural) Acetobacterium woodii (strain ATCC 29683 / DSM 1030 / JCM 2381 / KCTC 1655 / WB1) (bacteria)
Strain: ATCC 29683 / DSM 1030 / JCM 2381 / KCTC 1655 / WB1 / References: UniProt: H6LGM7, caffeoyl-CoA reductase
#3: Protein Caffeyl-CoA reductase-Etf complex subunit CarC / Caffeoyl-CoA reductase CarC / NADH-dependent caffeyl-CoA reduction


Mass: 41487.980 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: 1 FAD
Source: (natural) Acetobacterium woodii (strain ATCC 29683 / DSM 1030 / JCM 2381 / KCTC 1655 / WB1) (bacteria)
Strain: ATCC 29683 / DSM 1030 / JCM 2381 / KCTC 1655 / WB1 / References: UniProt: H6LGM6, caffeoyl-CoA reductase

-
Non-polymers , 3 types, 17 molecules

#4: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#5: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe4S4
#6: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.49 Å3/Da / Density % sol: 64.73 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: PEG 4000, Tris/HCl, Lithium sulphate

-
Data collection

DiffractionMean temperature: 100 K / Ambient temp details: 100
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 14, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 40990 / % possible obs: 98.8 % / Redundancy: 3.3 % / Net I/σ(I): 8.1
Reflection shellResolution: 3→3.1 Å

-
Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KPU, 4L1F

4kpu

4l1f


Resolution: 3.133→49.522 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 33.21
RfactorNum. reflection% reflection
Rfree0.2862 2057 5.05 %
Rwork0.2341 --
obs0.2368 40730 75.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.133→49.522 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15591 0 385 0 15976
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01316270
X-RAY DIFFRACTIONf_angle_d1.89722023
X-RAY DIFFRACTIONf_dihedral_angle_d5.26310439
X-RAY DIFFRACTIONf_chiral_restr0.12499
X-RAY DIFFRACTIONf_plane_restr0.0122767
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.133-3.20580.8161500.6149808X-RAY DIFFRACTION24
3.2058-3.2860.6287470.4504979X-RAY DIFFRACTION29
3.286-3.37480.4023570.36151174X-RAY DIFFRACTION34
3.3748-3.47410.359770.35081437X-RAY DIFFRACTION42
3.4741-3.58620.33491040.3241879X-RAY DIFFRACTION55
3.5862-3.71430.3741310.32732480X-RAY DIFFRACTION73
3.7143-3.8630.33791480.28932949X-RAY DIFFRACTION86
3.863-4.03870.33031780.26383223X-RAY DIFFRACTION94
4.0387-4.25160.29931840.23953388X-RAY DIFFRACTION99
4.2516-4.51780.28181880.22383367X-RAY DIFFRACTION99
4.5178-4.86630.25191780.19953413X-RAY DIFFRACTION99
4.8663-5.35550.27411900.20723414X-RAY DIFFRACTION99
5.3555-6.12920.2791910.22973394X-RAY DIFFRACTION99
6.1292-7.71750.28641610.22323391X-RAY DIFFRACTION98
7.7175-49.52830.20561730.17693377X-RAY DIFFRACTION96
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.70244.5147-4.66199.3711-1.55753.6383-0.5628-1.78922.6968-1.69811.5451-0.8774-0.57071.67-0.95331.9917-0.10850.07981.5938-0.40222.632-25.5941-119.2526-34.2627
23.34792.59250.27465.0589-0.92493.88972.4371-3.59352.04356.2041-0.99070.2959-1.28521.4441-1.454.3197-0.4483-0.20151.8444-0.4141.8991-14.4061-122.6428-30.4861
37.8229-4.43132.29732.949-1.64030.93620.99121.5123-2.36530.8136-2.14662.79651.3941-1.21911.07551.7908-0.43980.1682.5319-1.27392.6263-25.6145-103.5015-50.9461
47.99522.8949-4.78468.1093-0.42164.5578-0.34560.0332-1.2101-0.893-0.7921.1893-0.4747-0.07681.09251.6074-0.91070.04062.4569-0.56611.5024-39.7527-90.1969-53.1418
50.5085-0.94530.17321.7547-0.32190.0588-0.39892.2689-1.0382-1.24930.21241.33460.11190.29380.16822.2086-1.30510.15443.4453-1.0862.4265-44.5738-98.8521-46.0556
61.63721.71570.77133.66340.55421.3239-0.52640.9882-1.0288-0.92080.3989-0.08640.46670.0692-0.24770.8275-0.98370.01021.8151-0.2271.4748-34.2288-83.1893-39.0126
76.55252.4749-0.27765.5137-1.23714.1985-0.06470.8234-0.092-0.42420.394-0.4302-0.02570.2687-0.23160.9213-0.60670.23630.9219-0.29251.5741-22.1361-88.2119-18.1347
88.7775-7.4843-6.67766.8556.81437.7231-0.46010.6195-0.41380.73651.5308-2.68921.73070.6006-1.03011.3005-0.27270.10910.8521-0.31422.6898-17.3405-99.0162-17.6438
93.0731-3.55260.30186.78713.76947.04640.0249-0.14850.4381-1.80550.1549-0.9646-0.15820.2263-0.17982.0466-0.26020.54751.9049-1.38723.4774-21.3018-102.0569-29.3565
101.91761.09170.55254.4613-2.37312.5319-0.52330.8921-0.3516-1.16680.92550.14811.0643-0.2834-0.39811.4568-0.7510.34421.2292-0.38692.0887-29.8498-98.7369-25.7848
113.6806-3.20210.70513.32021.05195.32210.4459-1.6054-0.00130.9134-1.04051.16350.7165-1.25960.60551.1006-0.73780.06841.6731-0.5042.038-44.579-95.2951-18.4176
120.5331-0.14890.20730.11920.15670.66790.08310.0428-0.19330.0416-0.01570.09790.2462-0.1152-0.00560.8644-0.7378-0.03271.1118-0.03761.715-39.3537-90.0491-23.0304
136.06-3.8653-4.49176.14371.96493.9378-0.43721.3096-2.40481.2865-0.9643-0.9872.1287-0.81291.40471.3124-0.31380.16950.9493-0.25982.7671-16.4504-99.3854-11.2145
143.1413-3.82860.34846.4885-2.21012.33080.76021.4207-1.42960.3657-2.0774-0.12410.13481.23981.32261.1475-0.5910.50512.6885-0.70692.5178-13.0395-94.4391-38.7121
155.2002-3.6251-2.64255.84151.15211.4846-0.10231.60940.4393-0.2904-0.5816-0.108-0.2266-0.29950.66871.1449-0.7577-0.2912.68840.02511.1602-29.2415-58.9368-48.5341
169.6457-7.16176.96458.6825-3.73996.16231.59830.5558-3.1226-2.1296-0.42312.18651.30660.3786-1.15291.850.1003-0.15831.1944-0.14682.2044-25.681120.996634.627
175.2561-4.2083-3.53275.87924.01242.93270.88431.4501-2.615-4.06-1.16211.83732.5390.42760.28023.282-0.04850.21241.2576-0.5762.6908-14.699225.161831.0006
184.18125.4881.59668.02260.88462.39140.5016-2.09271.3173-1.009-1.01991.133-2.0534-1.28520.49871.82740.68450.31142.2918-0.44991.6381-26.23195.275850.6584
198.631.85542.95092.25440.64286.4362-0.6977-0.47480.4464-0.32370.06090.6117-0.993-0.83660.60331.50260.88130.01972.0970.61881.251-39.5389-11.731349.6223
205.44364.0782-1.56663.99341.35427.26160.7994-0.949-0.77561.795-0.1032-0.8511.55630.7998-0.73062.04050.96160.06282.25340.20631.2305-40.9347-4.818155.1197
217.045-1.45454.74569.39-3.22615.13920.0494-1.99770.25710.77340.12751.31871.50742.1005-0.17411.67141.10560.42813.02240.0281.7017-45.46580.458846.0224
221.2267-0.536-0.09712.54720.44320.6139-0.2431-0.47950.66050.55610.37820.1841-0.4053-0.24390.0670.85861.04070.16891.43370.47521.1051-34.4156-14.576839.0679
233.68560.66-0.11583.42370.81853.14390.2713-0.2181-0.1367-0.00880.1338-0.42050.32070.2648-0.0740.72290.59780.05230.57390.32171.1347-22.1884-9.332418.1375
245.06313.15693.63525.35774.45545.95880.4492-0.33480.5578-0.97130.1447-1.4961-0.7932-0.2957-0.50121.10240.27940.19730.65390.25011.9921-17.68441.237917.6799
259.10744.2092-3.4838.278-1.60741.3320.7317-0.93752.6036-0.80480.19410.6735-2.0981-0.3239-0.91811.53660.03830.53390.8082-0.25281.9062-21.60794.176429.4876
262.281-1.1145-0.09411.26330.06231.06720.0310.02440.5403-0.03630.0155-0.247-0.5252-0.1308-0.0091.15750.74590.15081.11050.30841.3614-30.04940.883825.7088
277.483-0.12970.01948.16844.6462.64390.00220.22760.3247-0.9868-0.52321.8322-0.4986-0.23820.52031.17790.80340.15051.72220.53551.6913-44.8201-2.706618.7864
280.36020.1703-0.45130.096-0.17620.7381-0.0349-0.02060.2882-0.02740.00060.0944-0.1679-0.16890.08920.77390.71030.05520.93110.35751.3355-39.5265-7.747123.0371
294.82462.40533.03562.93214.66357.6261-0.419-0.53731.9256-1.06590.1993-1.0474-2.6682-0.73010.22071.45330.37840.03450.69450.24072.0774-16.591.634211.2725
305.2685-3.61843.5863.8264-3.44394.28250.7805-1.07581.5909-2.3686-2.7988-2.48770.16550.30522.03051.20370.63350.03871.97960.30151.4501-13.3994-3.048738.479
313.20033.6113-0.21796.311-0.73565.44450.6712-1.14780.19720.6927-0.50060.4065-0.06640.2153-0.17761.16190.7060.33332.33880.42630.8584-28.7049-38.339649.0116
325.57630.638-1.20513.4348-0.92821.42610.0997-0.04270.67650.22770.3038-0.2771-0.2435-0.2258-0.25310.71750.2670.12840.3920.2720.8592-15.1737-18.79926.039
332.8148-1.5972.63184.1832-1.54883.9768-0.1607-0.1853-0.0017-0.15240.12520.4336-0.3011-0.36140.03420.29360.27480.03460.78370.54510.6272-33.0573-30.15672.2563
340.2041-0.1450.35980.22190.1892.1813-0.09760.32210.4047-0.45340.04270.2274-0.6165-0.17380.22490.56360.242-0.09030.59050.7940.7307-20.3418-22.3051-6.2028
350.0737-0.29160.1431.93790.85082.4725-0.05080.27690.3006-0.42840.03090.185-0.8077-0.3116-0.13460.5519-0.1164-0.2511.06420.96510.8448-27.3343-28.5173-23.247
360.6686-0.76171.35193.1062-2.164.8319-0.04160.23180.1158-0.071-0.1271-0.22220.00690.39170.2390.476-0-0.11370.91050.63980.5345-24.7204-30.3353-29.4199
370.4295-0.0451-0.52480.5731-0.02731.90360.01130.38370.3747-0.27670.13940.0992-0.367-0.1361-0.20860.3933-0.3713-0.16721.00020.75230.7222-29.3025-33.8511-21.942
381.2111-0.27960.06841.6352-0.52111.1465-0.07750.08030.40760.00310.48390.0067-0.1612-0.03980.5393-0.07950.4755-0.07580.14020.35280.2832-9.3392-35.85722.7217
390.24830.0511-0.29860.0842-0.09410.72130.01640.14230.0735-0.10320.28340.2816-0.1764-0.31490.2370.14570.0727-0.19330.43020.62030.4286-13.503-40.9017-5.5158
402.6593-0.21710.26815.29860.26441.589-0.11550.0828-0.36350.2548-0.0111-0.40210.41090.00540.0930.9237-0.316-0.07580.2953-0.02651.1072-15.8798-78.75-5.955
414.55492.191-2.40517.2521-0.12065.2706-0.31970.40310.3880.09160.47121.23660.4431-0.7049-0.20520.3298-0.1503-0.0470.67230.47930.8632-33.062-67.3989-1.868
421.39560.2505-0.57843.40990.3613.3552-0.0723-0.3299-0.54850.4610.0035-0.03860.9581-0.28050.25260.4788-0.18230.08060.28630.36090.8643-20.2055-75.22624.273
43-0.00760.0403-0.00991.4974-0.98421.8433-0.0254-0.2183-0.31380.3806-0.0140.07080.7784-0.0321-0.35190.71950.21710.17850.76240.99210.8525-25.6878-69.146824.883
440.08510.23090.27121.00150.10782.1640.0621-0.248-0.28190.42860.09040.02280.5569-0.1076-0.21150.46030.25170.07930.75660.78610.768-28.9153-63.83222.3371
451.19810.1679-0.11091.8906-0.51871.6181-0.19920.0096-0.54510.18070.2981-0.13040.24080.06360.2095-0.1106-0.346-0.12860.12530.2150.4015-9.3735-61.6858-2.6032
461.32180.51860.52961.0695-0.06641.74920.0268-0.1172-0.23020.04690.1920.23390.381-0.2417-0.19310.07340.06750.00530.29890.3770.4643-13.421-56.77395.6655
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'E' and (resid 12 through 42 )
2X-RAY DIFFRACTION2chain 'E' and (resid 43 through 59 )
3X-RAY DIFFRACTION3chain 'E' and (resid 60 through 76 )
4X-RAY DIFFRACTION4chain 'E' and (resid 77 through 123 )
5X-RAY DIFFRACTION5chain 'E' and (resid 124 through 142 )
6X-RAY DIFFRACTION6chain 'E' and (resid 143 through 329 )
7X-RAY DIFFRACTION7chain 'F' and (resid 1 through 75 )
8X-RAY DIFFRACTION8chain 'F' and (resid 76 through 93 )
9X-RAY DIFFRACTION9chain 'F' and (resid 94 through 105 )
10X-RAY DIFFRACTION10chain 'F' and (resid 106 through 144 )
11X-RAY DIFFRACTION11chain 'F' and (resid 145 through 158 )
12X-RAY DIFFRACTION12chain 'F' and (resid 159 through 187 )
13X-RAY DIFFRACTION13chain 'F' and (resid 188 through 213 )
14X-RAY DIFFRACTION14chain 'F' and (resid 214 through 231 )
15X-RAY DIFFRACTION15chain 'F' and (resid 232 through 256 )
16X-RAY DIFFRACTION16chain 'A' and (resid 12 through 42 )
17X-RAY DIFFRACTION17chain 'A' and (resid 43 through 59 )
18X-RAY DIFFRACTION18chain 'A' and (resid 60 through 76 )
19X-RAY DIFFRACTION19chain 'A' and (resid 77 through 96 )
20X-RAY DIFFRACTION20chain 'A' and (resid 97 through 123 )
21X-RAY DIFFRACTION21chain 'A' and (resid 124 through 142 )
22X-RAY DIFFRACTION22chain 'A' and (resid 143 through 329 )
23X-RAY DIFFRACTION23chain 'B' and (resid 1 through 75 )
24X-RAY DIFFRACTION24chain 'B' and (resid 76 through 93 )
25X-RAY DIFFRACTION25chain 'B' and (resid 94 through 105 )
26X-RAY DIFFRACTION26chain 'B' and (resid 106 through 144 )
27X-RAY DIFFRACTION27chain 'B' and (resid 145 through 158 )
28X-RAY DIFFRACTION28chain 'B' and (resid 159 through 187 )
29X-RAY DIFFRACTION29chain 'B' and (resid 188 through 213 )
30X-RAY DIFFRACTION30chain 'B' and (resid 214 through 231 )
31X-RAY DIFFRACTION31chain 'B' and (resid 232 through 256 )
32X-RAY DIFFRACTION32chain 'C' and (resid 1 through 20 )
33X-RAY DIFFRACTION33chain 'C' and (resid 21 through 47 )
34X-RAY DIFFRACTION34chain 'C' and (resid 48 through 99 )
35X-RAY DIFFRACTION35chain 'C' and (resid 100 through 163 )
36X-RAY DIFFRACTION36chain 'C' and (resid 164 through 191 )
37X-RAY DIFFRACTION37chain 'C' and (resid 192 through 229 )
38X-RAY DIFFRACTION38chain 'C' and (resid 230 through 341 )
39X-RAY DIFFRACTION39chain 'C' and (resid 342 through 378 )
40X-RAY DIFFRACTION40chain 'D' and (resid 1 through 20 )
41X-RAY DIFFRACTION41chain 'D' and (resid 21 through 47 )
42X-RAY DIFFRACTION42chain 'D' and (resid 48 through 90 )
43X-RAY DIFFRACTION43chain 'D' and (resid 91 through 191 )
44X-RAY DIFFRACTION44chain 'D' and (resid 192 through 229 )
45X-RAY DIFFRACTION45chain 'D' and (resid 230 through 341 )
46X-RAY DIFFRACTION46chain 'D' and (resid 342 through 378 )

+
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://pdbjlvh1.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