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- PDB-7z5o: W-formate dehydrogenase from Desulfovibrio vulgaris - Dithionite ... -

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Basic information

Entry
Database: PDB / ID: 7z5o
TitleW-formate dehydrogenase from Desulfovibrio vulgaris - Dithionite reduced form
Components(Formate dehydrogenase, ...) x 2
KeywordsOXIDOREDUCTASE / Formate / Carbon Dioxide / Dithionite
Function / homology
Function and homology information


formate dehydrogenase (cytochrome-c-553) activity / formate dehydrogenase / formate dehydrogenase (NAD+) activity / molybdopterin cofactor binding / cellular respiration / 4 iron, 4 sulfur cluster binding / periplasmic space / electron transfer activity / metal ion binding
Similarity search - Function
Formate dehydrogenase-N, alpha subunit / : / 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 / Molybdopterin dinucleotide-binding domain ...Formate dehydrogenase-N, alpha subunit / : / 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 / Molybdopterin dinucleotide-binding domain / Molydopterin dinucleotide binding domain / 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
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 str. Hildenborough (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.527 Å
AuthorsMota, C. / Oliveira, A.R. / Klymanska, K. / Pereira, I.C. / Romao, M.J.
Funding support Portugal, 1items
OrganizationGrant numberCountry
Fundacao para a Ciencia e a TecnologiaPTDC/BII-BBF/2050/2020 Portugal
CitationJournal: Acs Chem.Biol. / Year: 2022
Title: Spectroscopic and Structural Characterization of Reduced Desulfovibrio vulgaris Hildenborough W-FdhAB Reveals Stable Metal Coordination during Catalysis.
Authors: Oliveira, A.R. / Mota, C. / Klymanska, K. / Biaso, F. / Romao, M.J. / Guigliarelli, B. / Pereira, I.C.
History
DepositionMar 9, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 13, 2022Provider: repository / Type: Initial release
Revision 2.0Jul 20, 2022Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Derived calculations / Refinement description
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / diffrn_radiation_wavelength / diffrn_source / pdbx_entity_instance_feature / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_validate_close_contact / refine_ls_restr / software
Item: _atom_site_anisotrop.id / _diffrn_radiation_wavelength.wavelength ..._atom_site_anisotrop.id / _diffrn_radiation_wavelength.wavelength / _diffrn_source.pdbx_wavelength_list / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly_prop.value / _software.classification / _software.name / _software.version
Description: Atomic clashes / Provider: author / Type: Coordinate replacement
Revision 2.1Jul 27, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 2.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
AAA: Formate dehydrogenase, alpha subunit, selenocysteine-containing
BBB: Formate dehydrogenase, beta subunit, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,45721
Polymers138,3852
Non-polymers4,07219
Water13,007722
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11250 Å2
ΔGint-145 kcal/mol
Surface area37640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.811, 124.150, 149.666
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Formate dehydrogenase, ... , 2 types, 2 molecules AAABBB

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


Mass: 111903.430 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfovibrio vulgaris str. Hildenborough (bacteria)
Strain: ATCC 29579 / DSM 644 / NCIMB 8303 / VKM B-1760 / Hildenborough
Gene: fdnG-1, DVU_0587
Production host: Desulfovibrio vulgaris str. Hildenborough (bacteria)
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 genetically manipulated source
Source: (gene. exp.) Desulfovibrio vulgaris str. Hildenborough (bacteria)
Strain: Hildenborough / ATCC 29579 / DSM 644 / NCIMB 8303 / Gene: DVU_0588
Production host: Desulfovibrio vulgaris str. Hildenborough (bacteria)
References: UniProt: Q72EJ0

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Non-polymers , 8 types, 741 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-H2S / HYDROSULFURIC ACID / HYDROGEN SULFIDE


Mass: 34.081 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2S / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-W / TUNGSTEN ION


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


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


Mass: 62.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO3
#9: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


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


Mass: 18.015 Da / Num. of mol.: 722 / 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: 2.3 Å3/Da / Density % sol: 46.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8 / Details: 26% PEG 3350, 0.1 M Tris-HCl pH 8.0 and 1 M LiCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 8, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.527→95.737 Å / Num. obs: 182484 / % possible obs: 99.6 % / Redundancy: 4.5 % / CC1/2: 0.997 / Net I/σ(I): 9.8
Reflection shellResolution: 1.527→1.553 Å / Num. unique obs: 9070 / CC1/2: 0.591

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
autoPROCdata processing
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6sdv

6sdv


Resolution: 1.527→95.737 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.973 / SU B: 2.705 / SU ML: 0.041 / Cross valid method: FREE R-VALUE / ESU R: 0.065 / ESU R Free: 0.058
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1529 9121 4.998 %
Rwork0.1192 173354 -
all0.121 --
obs-182475 99.583 %
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.3 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 23.874 Å2
Baniso -1Baniso -2Baniso -3
1--0.234 Å2-0 Å2-0 Å2
2---0.28 Å20 Å2
3---0.514 Å2
Refinement stepCycle: LAST / Resolution: 1.527→95.737 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9211 0 191 722 10124
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0139660
X-RAY DIFFRACTIONr_bond_other_d0.0010.0178922
X-RAY DIFFRACTIONr_angle_refined_deg1.4151.6513137
X-RAY DIFFRACTIONr_angle_other_deg1.3891.58420600
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.74351175
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.11422.289485
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.224151555
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7671557
X-RAY DIFFRACTIONr_chiral_restr0.0830.21225
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0210880
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022220
X-RAY DIFFRACTIONr_nbd_refined0.2070.21731
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1790.28227
X-RAY DIFFRACTIONr_nbtor_refined0.1660.24666
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.24011
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1220.2474
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0410.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1860.215
X-RAY DIFFRACTIONr_nbd_other0.2370.243
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1140.213
X-RAY DIFFRACTIONr_mcbond_it2.0792.2934709
X-RAY DIFFRACTIONr_mcbond_other2.0783.0274708
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.527-1.5660.36480.28412737X-RAY DIFFRACTION99.7169
1.566-1.6090.2636450.23812434X-RAY DIFFRACTION99.7711
1.609-1.6560.2356360.19912025X-RAY DIFFRACTION99.74
1.656-1.7070.2026250.16411794X-RAY DIFFRACTION99.7911
1.707-1.7630.1715910.13111320X-RAY DIFFRACTION99.7571
1.763-1.8250.1545590.10411023X-RAY DIFFRACTION99.7245
1.825-1.8940.1355730.08910613X-RAY DIFFRACTION99.7414
1.894-1.9710.1345350.08410297X-RAY DIFFRACTION99.7238
1.971-2.0590.135500.0869722X-RAY DIFFRACTION99.6411
2.059-2.1590.1324940.0899464X-RAY DIFFRACTION99.7396
2.159-2.2760.1314880.0938884X-RAY DIFFRACTION99.4693
2.276-2.4140.1364340.0948532X-RAY DIFFRACTION99.6554
2.414-2.5810.1343970.0967977X-RAY DIFFRACTION99.4183
2.581-2.7870.1323920.0967423X-RAY DIFFRACTION99.2255
2.787-3.0530.1343520.1036873X-RAY DIFFRACTION99.3264
3.053-3.4130.1283300.1056229X-RAY DIFFRACTION99.0486
3.413-3.9410.1462930.1075495X-RAY DIFFRACTION99.2966
3.941-4.8260.1412710.124684X-RAY DIFFRACTION99.1793
4.826-6.8210.1821930.1833696X-RAY DIFFRACTION99.1333
6.821-95.7370.2211150.1882132X-RAY DIFFRACTION98.4231

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