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- PDB-6elq: Carbon Monoxide Dehydrogenase IV from Carboxydothermus hydrogenof... -

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Basic information

Entry
Database: PDB / ID: 6elq
TitleCarbon Monoxide Dehydrogenase IV from Carboxydothermus hydrogenoformans
ComponentsCarbon Monoxide Dehydrogenase
KeywordsOXIDOREDUCTASE / Anaerobiosis / Carbon Dioxide / Carbon Monoxide / Crystallization / Iron / Ligands / Nickel / Recombinant Proteins
Function / homology
Function and homology information


anaerobic carbon monoxide dehydrogenase / anaerobic carbon-monoxide dehydrogenase activity / : / hydroxylamine reductase activity / nickel cation binding / generation of precursor metabolites and energy / peroxidase activity / response to hydrogen peroxide / 4 iron, 4 sulfur cluster binding
Similarity search - Function
Substrate Binding Domain Of Dnak; Chain:A; Domain 2 - #30 / Rossmann fold - #2030 / 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 / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / Up-down Bundle ...Substrate Binding Domain Of Dnak; Chain:A; Domain 2 - #30 / Rossmann fold - #2030 / 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 / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
FE(4)-NI(1)-S(5) CLUSTER with Oxygen / IRON/SULFUR CLUSTER / Carbon monoxide dehydrogenase
Similarity search - Component
Biological speciesCarboxydothermus hydrogenoformans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.52 Å
AuthorsDomnik, L. / Goetzl, S. / Jeoung, J.H. / Dobbek, H.
CitationJournal: Angew. Chem. Int. Ed. Engl. / Year: 2017
Title: CODH-IV: A High-Efficiency CO-Scavenging CO Dehydrogenase with Resistance to O2.
Authors: Domnik, L. / Merrouch, M. / Goetzl, S. / Jeoung, J.H. / Leger, C. / Dementin, S. / Fourmond, V. / Dobbek, H.
History
DepositionSep 29, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 3, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.2May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
X: Carbon Monoxide Dehydrogenase
A: Carbon Monoxide Dehydrogenase
B: Carbon Monoxide Dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)208,05411
Polymers205,0173
Non-polymers3,0378
Water4,288238
1
X: Carbon Monoxide Dehydrogenase
A: Carbon Monoxide Dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,5857
Polymers136,6782
Non-polymers1,9085
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8490 Å2
ΔGint-89 kcal/mol
Surface area38580 Å2
MethodPISA
2
B: Carbon Monoxide Dehydrogenase
hetero molecules

B: Carbon Monoxide Dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,9378
Polymers136,6782
Non-polymers2,2596
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_675x-y+1,-y+2,-z1
Buried area7990 Å2
ΔGint-68 kcal/mol
Surface area39890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)209.150, 209.150, 93.410
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11A-5175-

HOH

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Components

#1: Protein Carbon Monoxide Dehydrogenase / Carbon Monoxide Dehydrogenase 4


Mass: 68338.883 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Carboxydothermus hydrogenoformans (bacteria)
Gene: cooSIV / Production host: Escherichia coli (E. coli)
References: UniProt: Q3AE44, anaerobic carbon monoxide dehydrogenase
#2: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Fe4S4
#3: Chemical ChemComp-BF8 / FE(4)-NI(1)-S(5) CLUSTER with Oxygen


Mass: 426.333 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe4NiOS4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 238 / Source method: isolated from a natural source / Formula: H2O

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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: 2.88 Å3/Da / Density % sol: 57.24 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 20 % (v/v) Polypropoylene glycol 400, 10 % (v/v) 1-Propanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.52→46.7 Å / Num. obs: 79240 / % possible obs: 99.95 % / Redundancy: 15.9 % / Net I/σ(I): 10.5

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Processing

Software
NameVersionClassification
PHENIX(1.11.1-2575_1168: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.52→45.626 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 30.95
RfactorNum. reflection% reflection
Rfree0.2747 2111 2.67 %
Rwork0.2352 --
obs0.2362 79170 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.52→45.626 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14286 0 70 238 14594
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00314681
X-RAY DIFFRACTIONf_angle_d0.53419959
X-RAY DIFFRACTIONf_dihedral_angle_d17.1748964
X-RAY DIFFRACTIONf_chiral_restr0.0462376
X-RAY DIFFRACTIONf_plane_restr0.0032556
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.52-2.57860.331380.33475084X-RAY DIFFRACTION100
2.5786-2.64310.36351380.31725092X-RAY DIFFRACTION100
2.6431-2.71460.31021400.31685107X-RAY DIFFRACTION100
2.7146-2.79440.36791400.30465107X-RAY DIFFRACTION100
2.7944-2.88460.29011390.28475058X-RAY DIFFRACTION100
2.8846-2.98770.3351400.27665114X-RAY DIFFRACTION100
2.9877-3.10730.31271410.27835130X-RAY DIFFRACTION100
3.1073-3.24870.30241400.26195112X-RAY DIFFRACTION100
3.2487-3.41990.27821410.25395140X-RAY DIFFRACTION100
3.4199-3.63410.26441400.23615106X-RAY DIFFRACTION100
3.6341-3.91450.27041400.22635140X-RAY DIFFRACTION100
3.9145-4.30820.24781420.20315154X-RAY DIFFRACTION100
4.3082-4.9310.19991420.1855183X-RAY DIFFRACTION100
4.931-6.210.23791430.22515210X-RAY DIFFRACTION100
6.21-45.63320.29861470.20815322X-RAY DIFFRACTION100

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