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- PDB-6sdr: W-formate dehydrogenase from Desulfovibrio vulgaris - Oxidized form -

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Basic information

Entry
Database: PDB / ID: 6sdr
TitleW-formate dehydrogenase from Desulfovibrio vulgaris - Oxidized form
Components(Formate dehydrogenase, ...) x 2
KeywordsELECTRON TRANSPORT
Function / homology
Function and homology information


formate dehydrogenase (cytochrome-c-553) activity / formate dehydrogenase / formate dehydrogenase (NAD+) activity / molybdenum ion binding / molybdopterin cofactor binding / cell envelope / anaerobic respiration / 4 iron, 4 sulfur cluster binding / periplasmic space / electron transfer activity / metal ion binding
Similarity search - Function
Formate dehydrogenase-N, alpha subunit / : / Rossmann fold - #740 / Dimethylsulfoxide Reductase; domain 2 / Dimethylsulfoxide Reductase, domain 2 / 4Fe-4S dicluster domain / Molybdopterin oxidoreductase, molybdopterin cofactor binding site / Prokaryotic molybdopterin oxidoreductases signature 1. / Prokaryotic molybdopterin oxidoreductases signature 3. / Molybdopterin oxidoreductase, prokaryotic, conserved site ...Formate dehydrogenase-N, alpha subunit / : / Rossmann fold - #740 / Dimethylsulfoxide Reductase; domain 2 / Dimethylsulfoxide Reductase, domain 2 / 4Fe-4S dicluster domain / Molybdopterin oxidoreductase, molybdopterin cofactor binding site / Prokaryotic molybdopterin oxidoreductases signature 1. / Prokaryotic molybdopterin oxidoreductases signature 3. / Molybdopterin oxidoreductase, prokaryotic, conserved site / Molybdopterin oxidoreductase Fe4S4 domain / Molybdopterin oxidoreductase Fe4S4 domain / Alpha-Beta Plaits - #20 / Molybdopterin dinucleotide-binding domain / Molydopterin dinucleotide binding domain / Barwin-like endoglucanases - #20 / Barwin-like endoglucanases / Twin-arginine translocation pathway, signal sequence, bacterial/archaeal / Aspartate decarboxylase-like domain superfamily / Molybdopterin oxidoreductase, 4Fe-4S domain / Prokaryotic molybdopterin oxidoreductases 4Fe-4S domain profile. / Molybdopterin oxidoreductase / Molybdopterin oxidoreductase / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / Alpha-Beta Plaits / Beta Barrel / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
HYDROSULFURIC ACID / Chem-MGD / IRON/SULFUR CLUSTER / : / Formate dehydrogenase, beta subunit, putative / Formate dehydrogenase, alpha subunit, selenocysteine-containing
Similarity search - Component
Biological speciesDesulfovibrio vulgaris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsOliveira, A.R. / Mota, C. / Mourato, C. / Domingos, R.M. / Santos, M.F.A. / Gesto, D. / Guigliarelli, B. / Santos-Silva, T. / Romao, M.J. / Pereira, I.C.
Funding support Portugal, 2items
OrganizationGrant numberCountry
Fundacao para a Ciencia e a TecnologiaPTDC/BBB-EBB/2723/2014 Portugal
Fundacao para a Ciencia e a TecnologiaUID/Multi/04378/2019 Portugal
CitationJournal: Acs Catalysis / Year: 2020
Title: Towards the mechanistic understanding of enzymatic CO2 reduction
Authors: Oliveira, A.R. / Mota, C. / Mourato, C. / Domingos, R.M. / Santos, M.F.A. / Gesto, D. / Guigliarelli, B. / Santos-Silva, T. / Romao, M.J. / Pereira, I.C.
History
DepositionJul 29, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 11, 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Formate dehydrogenase, alpha subunit, selenocysteine-containing
B: Formate dehydrogenase, beta subunit, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,44215
Polymers137,8762
Non-polymers3,56613
Water10,557586
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10010 Å2
ΔGint-149 kcal/mol
Surface area36540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.593, 127.644, 148.213
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Formate dehydrogenase, ... , 2 types, 2 molecules AB

#1: Protein Formate dehydrogenase, alpha subunit, selenocysteine-containing


Mass: 111394.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Desulfovibrio vulgaris (strain Hildenborough / ATCC 29579 / DSM 644 / NCIMB 8303) (bacteria)
Strain: Hildenborough / ATCC 29579 / DSM 644 / NCIMB 8303 / References: UniProt: Q72EJ1, formate dehydrogenase
#2: Protein Formate dehydrogenase, beta subunit, putative


Mass: 26481.494 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Desulfovibrio vulgaris (strain Hildenborough / ATCC 29579 / DSM 644 / NCIMB 8303) (bacteria)
Strain: Hildenborough / ATCC 29579 / DSM 644 / NCIMB 8303 / References: UniProt: Q72EJ0

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Non-polymers , 6 types, 599 molecules

#3: Chemical ChemComp-MGD / 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE / MOLYBDOPTERIN GUANOSINE DINUCLEOTIDE


Mass: 740.557 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H26N10O13P2S2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe4S4
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-H2S / HYDROSULFURIC ACID / HYDROGEN SULFIDE


Mass: 34.081 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2S / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-W / TUNGSTEN ION


Mass: 183.840 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: W / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 586 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.35 Å3/Da / Density % sol: 47.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 32% PEG 3350, 0.1M Tris-HCl pH 8.5, 1M LiCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→49.4 Å / Num. obs: 136041 / % possible obs: 99.2 % / Redundancy: 5.4 % / Biso Wilson estimate: 25.35 Å2 / CC1/2: 0.99 / Net I/σ(I): 9.3
Reflection shellResolution: 2.1→2.15 Å / Num. unique obs: 4590 / CC1/2: 0.72

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1H0H

1h0h


Resolution: 2.1→48.36 Å / SU ML: 0.244 / Cross valid method: FREE R-VALUE / σ(F): 0.01 / Phase error: 24.2511
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2257 6777 5 %
Rwork0.1855 128707 -
obs0.1875 135484 98.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.3 Å2
Refinement stepCycle: LAST / Resolution: 2.1→48.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9198 0 158 586 9942
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00429634
X-RAY DIFFRACTIONf_angle_d0.687613114
X-RAY DIFFRACTIONf_chiral_restr0.04721381
X-RAY DIFFRACTIONf_plane_restr0.00411683
X-RAY DIFFRACTIONf_dihedral_angle_d14.40711298
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.120.32372670.30374324X-RAY DIFFRACTION99.05
2.12-2.150.32172710.28544288X-RAY DIFFRACTION98.72
2.15-2.180.30252150.2634269X-RAY DIFFRACTION98.55
2.18-2.20.26772530.25494299X-RAY DIFFRACTION98.59
2.2-2.230.29522030.25384373X-RAY DIFFRACTION98.28
2.23-2.260.28542050.24884230X-RAY DIFFRACTION97.77
2.26-2.290.26812150.244307X-RAY DIFFRACTION97.54
2.29-2.330.29161970.24374258X-RAY DIFFRACTION96.91
2.33-2.370.28772160.22814331X-RAY DIFFRACTION98.31
2.37-2.40.25191640.22644362X-RAY DIFFRACTION98.41
2.4-2.450.23952050.2314320X-RAY DIFFRACTION98.2
2.45-2.490.27852390.22544306X-RAY DIFFRACTION98.16
2.49-2.540.2992300.21954271X-RAY DIFFRACTION98.36
2.54-2.590.27152310.20534278X-RAY DIFFRACTION97.89
2.59-2.650.21542450.20994271X-RAY DIFFRACTION97.79
2.65-2.710.26312340.20624300X-RAY DIFFRACTION98.24
2.71-2.780.26862730.2024214X-RAY DIFFRACTION97.99
2.78-2.850.26952180.21214314X-RAY DIFFRACTION97.97
2.85-2.930.25962280.21934298X-RAY DIFFRACTION97.29
2.93-3.030.27882080.2254225X-RAY DIFFRACTION97.64
3.03-3.140.29492460.20514273X-RAY DIFFRACTION98.24
3.14-3.260.23181960.19654349X-RAY DIFFRACTION98.19
3.26-3.410.21332110.17334310X-RAY DIFFRACTION98.26
3.41-3.590.20851970.16314355X-RAY DIFFRACTION98.57
3.59-3.820.18612510.1474287X-RAY DIFFRACTION98.61
3.82-4.110.16752220.13584309X-RAY DIFFRACTION98.69
4.11-4.520.15262630.12334258X-RAY DIFFRACTION98.37
4.52-5.180.17522480.12374282X-RAY DIFFRACTION98.16
5.18-6.520.18872150.14754288X-RAY DIFFRACTION97.3
6.52-48.360.14472110.14054158X-RAY DIFFRACTION95.21
Refinement TLS params.Method: refined / Origin x: -16.3454038738 Å / Origin y: -11.4537754875 Å / Origin z: 29.7578689737 Å
111213212223313233
T0.147728289141 Å20.00817239330521 Å2-0.0743868169942 Å2-0.166399830021 Å2-0.0209669484311 Å2--0.207061564479 Å2
L0.818163677477 °2-0.506475859193 °20.375908723009 °2-1.71690243579 °2-0.503442621071 °2--1.76207976328 °2
S0.114296293963 Å °-0.00205270146135 Å °-0.0525180042687 Å °-0.191424248387 Å °0.0692455663148 Å °0.198721337401 Å °0.297250266161 Å °0.0207993451418 Å °-0.098917782624 Å °
Refinement TLS groupSelection details: all

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