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- PDB-6vwz: Crystal structure of air-exposed C45G/T50C D. vulgaris carbon mon... -

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Basic information

Entry
Database: PDB / ID: 6vwz
TitleCrystal structure of air-exposed C45G/T50C D. vulgaris carbon monoxide dehydrogenase (20 minute air exposure)
ComponentsCarbon monoxide dehydrogenase
KeywordsOXIDOREDUCTASE / nickel-iron-sulfur (Ni-Fe-S) cluster / iron-sulfur (Fe-S) cluster / metalloenzyme
Function / homology
Function and homology information


anaerobic carbon monoxide dehydrogenase / carbon-monoxide dehydrogenase (ferredoxin) activity / carbon-monoxide dehydrogenase (acceptor) activity / hydroxylamine reductase activity / nickel cation binding / generation of precursor metabolites and energy / peroxidase activity / response to hydrogen peroxide / 2 iron, 2 sulfur cluster binding / 4 iron, 4 sulfur cluster binding
Similarity search - Function
Ni-containing CO dehydrogenase / CO dehydrogenase, alpha-bundle / Hydroxylamine reductase/Ni-containing CO dehydrogenase / Prismane/CO dehydrogenase family / Prismane-like, alpha/beta-sandwich / Prismane-like superfamily
Similarity search - Domain/homology
Fe(4)-Ni(1)-S(4) cluster, oxidized / IRON/SULFUR CLUSTER / Carbon monoxide dehydrogenase
Similarity search - Component
Biological speciesDesulfovibrio vulgaris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.488 Å
AuthorsWittenborn, E.C. / Drennan, C.L.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM069857 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM126982 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32 GM008334 United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Acs Catalysis / Year: 2020
Title: The Solvent-Exposed Fe-S D-Cluster Contributes to Oxygen-Resistance inDesulfovibrio vulgarisNi-Fe Carbon Monoxide Dehydrogenase.
Authors: Wittenborn, E.C. / Guendon, C. / Merrouch, M. / Benvenuti, M. / Fourmond, V. / Leger, C. / Drennan, C.L. / Dementin, S.
History
DepositionFeb 20, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Carbon monoxide dehydrogenase
B: Carbon monoxide dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,3818
Polymers133,4132
Non-polymers1,9686
Water6,323351
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8980 Å2
ΔGint-95 kcal/mol
Surface area36210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.730, 112.000, 195.420
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 5 through 27 or (resid 28...
21(chain B and ((resid 5 and (name N or name...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSGLYGLY(chain A and (resid 5 through 27 or (resid 28...AA5 - 275 - 27
12ILEILESERSER(chain A and (resid 5 through 27 or (resid 28...AA28 - 2928 - 29
13LYSLYSSERSER(chain A and (resid 5 through 27 or (resid 28...AA5 - 6295 - 629
14LYSLYSSERSER(chain A and (resid 5 through 27 or (resid 28...AA5 - 6295 - 629
15LYSLYSSERSER(chain A and (resid 5 through 27 or (resid 28...AA5 - 6295 - 629
16LYSLYSSERSER(chain A and (resid 5 through 27 or (resid 28...AA5 - 6295 - 629
21LYSLYSLYSLYS(chain B and ((resid 5 and (name N or name...BB55
22SERSERSERSER(chain B and ((resid 5 and (name N or name...BB4 - 6294 - 629
23SERSERSERSER(chain B and ((resid 5 and (name N or name...BB4 - 6294 - 629
24SERSERSERSER(chain B and ((resid 5 and (name N or name...BB4 - 6294 - 629
25SERSERSERSER(chain B and ((resid 5 and (name N or name...BB4 - 6294 - 629

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Components

#1: Protein Carbon monoxide dehydrogenase /


Mass: 66706.711 Da / Num. of mol.: 2 / Mutation: C45G/T50C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfovibrio vulgaris (strain Hildenborough / ATCC 29579 / DSM 644 / NCIMB 8303) (bacteria)
Strain: Hildenborough / ATCC 29579 / DSM 644 / NCIMB 8303 / Gene: cooS, DVU_2098 / Production host: Desulfovibrio fructosivorans JJ (bacteria)
References: UniProt: Q72A99, anaerobic carbon monoxide dehydrogenase
#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CUV / Fe(4)-Ni(1)-S(4) cluster, oxidized / C cluster, oxidized / Redox


Mass: 410.333 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4NiS4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 351 / Source method: isolated from a natural source / Formula: H2O
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: 2.7 Å3/Da / Density % sol: 54.37 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop
Details: 1.0-1.1 M ammonium tartrate dibasic, pH 7, 6-9% v/v glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 8, 2016
RadiationMonochromator: Cryo-cooled double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.488→100 Å / Num. obs: 50165 / % possible obs: 99.5 % / Redundancy: 4.7 % / CC1/2: 0.983 / Net I/σ(I): 6.8
Reflection shellResolution: 2.488→2.55 Å / Num. unique obs: 3647 / CC1/2: 0.666

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6B6V

6b6v


Resolution: 2.488→73.629 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 20.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2112 2176 4.34 %
Rwork0.1809 47979 -
obs0.1823 50155 97.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 77.47 Å2 / Biso mean: 27.0342 Å2 / Biso min: 12.23 Å2
Refinement stepCycle: final / Resolution: 2.488→73.629 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9183 0 48 351 9582
Biso mean--37.65 29.71 -
Num. residues----1251
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0059437
X-RAY DIFFRACTIONf_angle_d1.14612902
X-RAY DIFFRACTIONf_chiral_restr0.0431498
X-RAY DIFFRACTIONf_plane_restr0.0041680
X-RAY DIFFRACTIONf_dihedral_angle_d18.2675721
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5623X-RAY DIFFRACTION4.907TORSIONAL
12B5623X-RAY DIFFRACTION4.907TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.4883-2.54240.2954900.2307199265
2.5424-2.60150.25461360.2306299499
2.6015-2.66660.30651350.2186301399
2.6666-2.73870.24871440.21173042100
2.7387-2.81930.22541330.19473014100
2.8193-2.91030.25071380.19463031100
2.9103-3.01430.22911390.19063060100
3.0143-3.1350.23831390.18883047100
3.135-3.27770.20351360.1847304099
3.2777-3.45050.21191370.1682303399
3.4505-3.66660.16971400.16093063100
3.6666-3.94970.18931380.15553060100
3.9497-4.34720.18251410.15223104100
4.3472-4.97610.17061380.1605307999
4.9761-6.26880.21761420.2045313299
6.2688-73.6290.21191500.1832327599

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