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- PDB-6vx0: Crystal structure of air-exposed C45G/T50C D. vulgaris carbon mon... -

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Basic information

Entry
Database: PDB / ID: 6vx0
TitleCrystal structure of air-exposed C45G/T50C D. vulgaris carbon monoxide dehydrogenase (2 hour 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 / hydroxylamine reductase activity / anaerobic carbon-monoxide dehydrogenase 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: 2.21 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)135,0297
Polymers133,4132
Non-polymers1,6165
Water12,322684
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8600 Å2
ΔGint-75 kcal/mol
Surface area36370 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 4 through 5 and (name N...
21(chain B and ((resid 4 through 5 and (name N...

NCS domain segments:

Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER

Dom-IDComponent-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYS(chain A and ((resid 4 through 5 and (name N...AA4 - 54 - 5
12SERSER(chain A and ((resid 4 through 5 and (name N...AA4 - 6294 - 629
13SERSER(chain A and ((resid 4 through 5 and (name N...AA4 - 6294 - 629
14SERSER(chain A and ((resid 4 through 5 and (name N...AA4 - 6294 - 629
15SERSER(chain A and ((resid 4 through 5 and (name N...AA4 - 6294 - 629
21LYSLYS(chain B and ((resid 4 through 5 and (name N...BB4 - 54 - 5
22LEULEU(chain B and ((resid 4 through 5 and (name N...BB4 - 6274 - 627
23LEULEU(chain B and ((resid 4 through 5 and (name N...BB4 - 6274 - 627
24LEULEU(chain B and ((resid 4 through 5 and (name N...BB4 - 6274 - 627
25LEULEU(chain B and ((resid 4 through 5 and (name N...BB4 - 6274 - 627

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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


Mass: 351.640 Da / Num. of mol.: 2 / 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


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


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


Mass: 18.015 Da / Num. of mol.: 684 / 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: 0.9791 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: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.21→100 Å / Num. obs: 72260 / % possible obs: 99.8 % / Redundancy: 5.3 % / CC1/2: 0.995 / Net I/σ(I): 10.1
Reflection shellResolution: 2.21→2.26 Å / Num. unique obs: 5304 / CC1/2: 0.683

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6B6V

6b6v


Resolution: 2.21→97.71 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 19.32
RfactorNum. reflection% reflection
Rfree0.2028 3143 4.35 %
Rwork0.1744 --
obs0.1757 72251 99.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 81.26 Å2 / Biso mean: 31.8388 Å2 / Biso min: 14.31 Å2
Refinement stepCycle: final / Resolution: 2.21→97.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9188 0 40 684 9912
Biso mean--39.08 37.05 -
Num. residues----1250
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5531X-RAY DIFFRACTION4.943TORSIONAL
12B5531X-RAY DIFFRACTION4.943TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 22

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.21-2.250.30471300.24362801293190
2.25-2.290.27791410.236831223263100
2.29-2.320.27281410.231230943235100
2.32-2.370.28641420.210531263268100
2.37-2.410.22351420.210531193261100
2.41-2.460.25231420.208731133255100
2.46-2.520.22791410.20413113325499
2.52-2.570.25051410.198831323273100
2.57-2.640.20591440.189731293273100
2.64-2.710.21841440.188631283272100
2.71-2.790.20241390.188331293268100
2.79-2.880.23221440.18431663310100
2.88-2.980.21231400.178531433283100
2.98-3.10.21111440.175331403284100
3.1-3.240.17371410.17693122326399
3.24-3.410.20681450.160731553300100
3.41-3.630.1631420.152231673309100
3.63-3.910.18361440.145831943338100
3.91-4.30.17031470.139131793326100
4.3-4.920.16021460.14013201334799
4.92-6.20.18281480.178632623410100
6.2-97.710.21661550.18173373352899

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