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- PDB-6sdv: W-formate dehydrogenase from Desulfovibrio vulgaris - Formate red... -

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Basic information

Entry
Database: PDB / ID: 6sdv
TitleW-formate dehydrogenase from Desulfovibrio vulgaris - Formate reduced 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 / cellular respiration / molybdopterin cofactor binding / 4 iron, 4 sulfur cluster binding / electron transfer activity / periplasmic space / metal ion binding
Similarity search - Function
Formate dehydrogenase-N, alpha subunit / Dimethylsulfoxide Reductase; domain 2 / Dimethylsulfoxide Reductase, domain 2 / Rossmann fold - #740 / 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 ...Formate dehydrogenase-N, alpha subunit / Dimethylsulfoxide Reductase; domain 2 / Dimethylsulfoxide Reductase, domain 2 / Rossmann fold - #740 / 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 / NITRATE ION / DI(HYDROXYETHYL)ETHER / IRON/SULFUR CLUSTER / : / Formate dehydrogenase, beta subunit, putative / Formate dehydrogenase, alpha subunit, selenocysteine-containing
Similarity search - Component
Biological speciesDesulfovibrio vulgaris (bacteria)
Desulfovibrio vulgaris str. Hildenborough (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)142,64223
Polymers138,3852
Non-polymers4,25721
Water13,836768
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11600 Å2
ΔGint-146 kcal/mol
Surface area37180 Å2
Unit cell
Length a, b, c (Å)64.885, 128.560, 149.629
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,Formate dehydrogenase, alpha subunit, selenocysteine-containing,W-formate dehydrogenase - alpha subunit /


Mass: 111903.430 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), (natural) Desulfovibrio vulgaris str. Hildenborough (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 , 8 types, 789 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 / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe4S4
#5: Chemical ChemComp-W / TUNGSTEN ION


Mass: 183.840 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: W / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-H2S / HYDROSULFURIC ACID / HYDROGEN SULFIDE / 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical ChemComp-NO3 / NITRATE ION / Nitrate


Mass: 62.005 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: NO3
#9: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#10: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 768 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.38 Å3/Da / Density % sol: 48.24 %
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: ID30B / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 13, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.9→48.76 Å / Num. obs: 188388 / % possible obs: 99.7 % / Redundancy: 4.5 % / Biso Wilson estimate: 21.88 Å2 / CC1/2: 0.994 / Net I/σ(I): 7.9
Reflection shellResolution: 1.9→1.93 Å / Mean I/σ(I) obs: 1.4 / Num. unique obs: 4813 / CC1/2: 0.484

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6SDR

6sdr


Resolution: 1.9→48.76 Å / SU ML: 0.2304 / Cross valid method: FREE R-VALUE / σ(F): 0.01 / Phase error: 20.6125
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1965 9299 4.94 %
Rwork0.1594 179089 -
obs0.1613 188388 98.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.02 Å2
Refinement stepCycle: LAST / Resolution: 1.9→48.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9234 0 203 768 10205
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00959694
X-RAY DIFFRACTIONf_angle_d1.003613180
X-RAY DIFFRACTIONf_chiral_restr0.0621383
X-RAY DIFFRACTIONf_plane_restr0.00651686
X-RAY DIFFRACTIONf_dihedral_angle_d14.23711311
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.920.35582700.31776035X-RAY DIFFRACTION98.62
1.92-1.940.33173200.28665882X-RAY DIFFRACTION98.02
1.94-1.970.30982970.26915974X-RAY DIFFRACTION98.23
1.97-1.990.25823000.25735884X-RAY DIFFRACTION98.47
1.99-2.020.27463280.24495997X-RAY DIFFRACTION99.04
2.02-2.050.28253110.24265865X-RAY DIFFRACTION98.42
2.05-2.080.30772940.25126048X-RAY DIFFRACTION98.95
2.08-2.110.24943040.22566017X-RAY DIFFRACTION99.57
2.11-2.140.25412930.21365959X-RAY DIFFRACTION98.74
2.14-2.170.24872830.20456025X-RAY DIFFRACTION99.03
2.17-2.210.22573280.19415948X-RAY DIFFRACTION98.94
2.21-2.250.23423270.19945961X-RAY DIFFRACTION98.53
2.25-2.30.22152690.19136009X-RAY DIFFRACTION99.15
2.3-2.340.223250.17585937X-RAY DIFFRACTION98.38
2.34-2.390.20293000.16875942X-RAY DIFFRACTION97.94
2.39-2.450.20513270.16695893X-RAY DIFFRACTION98.89
2.45-2.510.20723170.15956031X-RAY DIFFRACTION99.53
2.51-2.580.20293180.15576004X-RAY DIFFRACTION99.22
2.58-2.650.20443080.14935994X-RAY DIFFRACTION99.7
2.65-2.740.20383370.15046000X-RAY DIFFRACTION99.62
2.74-2.840.18553400.14455985X-RAY DIFFRACTION99.34
2.84-2.950.19953150.13926027X-RAY DIFFRACTION99.26
2.95-3.090.17543390.13825924X-RAY DIFFRACTION98.91
3.09-3.250.16653230.13245964X-RAY DIFFRACTION99.16
3.25-3.450.18042850.12635992X-RAY DIFFRACTION99.24
3.45-3.720.16242910.12626025X-RAY DIFFRACTION99.34
3.72-4.090.15052920.11436006X-RAY DIFFRACTION99.07
4.09-4.680.12473120.11055983X-RAY DIFFRACTION98.85
4.68-5.90.17263430.13525953X-RAY DIFFRACTION99.12
5.9-48.760.17683030.15055825X-RAY DIFFRACTION96.69
Refinement TLS params.Method: refined / Origin x: -16.0802007908 Å / Origin y: -11.8230556213 Å / Origin z: 30.1252697442 Å
111213212223313233
T0.121638762752 Å20.00634448494726 Å2-0.0265152027755 Å2-0.142589205122 Å2-0.0183415318419 Å2--0.159685431492 Å2
L0.393743892504 °2-0.12845545246 °20.00887639815995 °2-0.840663422803 °2-0.219966290046 °2--0.485876393077 °2
S0.00725578232062 Å °0.0414779819146 Å °0.0147617753997 Å °-0.0992863635379 Å °0.0180135416179 Å °0.112398411657 Å °0.0487707828567 Å °-0.0419665677617 Å °-0.0137724509894 Å °
Refinement TLS groupSelection details: all

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