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- PDB-8x9h: Crystal structure of CO dehydrogenase mutant (F41C) -

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Basic information

Entry
Database: PDB / ID: 8x9h
TitleCrystal structure of CO dehydrogenase mutant (F41C)
ComponentsCarbon monoxide dehydrogenase 2
KeywordsELECTRON TRANSPORT / OXIDOREDUCTASE
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 / 4 iron, 4 sulfur cluster binding / plasma membrane / cytoplasm
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
: / FE2/S2 (INORGANIC) CLUSTER / IRON/SULFUR CLUSTER / FE(4)-NI(1)-S(4) CLUSTER / Carbon monoxide dehydrogenase 2
Similarity search - Component
Biological speciesCarboxydothermus hydrogenoformans Z-2901 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsLee, H.H. / Heo, Y. / Yoon, H.J. / Kim, S.M. / Kong, S.Y.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
Other government Korea, Republic Of
CitationJournal: Nat Commun / Year: 2024
Title: Identifying a key spot for electron mediator-interaction to tailor CO dehydrogenase's affinity.
Authors: Kim, S.M. / Kang, S.H. / Lee, J. / Heo, Y. / Poloniataki, E.G. / Kang, J. / Yoon, H.J. / Kong, S.Y. / Yun, Y. / Kim, H. / Ryu, J. / Lee, H.H. / Kim, Y.H.
History
DepositionNov 30, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 17, 2024Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Database references / Category: citation
Item: _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Carbon monoxide dehydrogenase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,1135
Polymers69,1201
Non-polymers9944
Water6,377354
1
A: Carbon monoxide dehydrogenase 2
hetero molecules

A: Carbon monoxide dehydrogenase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,22710
Polymers138,2402
Non-polymers1,9878
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation1
MethodPISA
Unit cell
Length a, b, c (Å)112.281, 75.390, 70.792
Angle α, β, γ (deg.)90.00, 111.18, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1069-

HOH

21A-1070-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Carbon monoxide dehydrogenase 2 / CODH 2


Mass: 69119.844 Da / Num. of mol.: 1 / Mutation: F41C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Carboxydothermus hydrogenoformans Z-2901 (bacteria)
Strain: Z-2901 / Gene: cooS2 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9F8A8, anaerobic carbon monoxide dehydrogenase

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Non-polymers , 5 types, 358 molecules

#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4
#3: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2
#4: Chemical ChemComp-XCC / FE(4)-NI(1)-S(4) CLUSTER / C CLUSTER


Mass: 410.333 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4NiS4
#5: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 354 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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 Å3/Da / Density % sol: 38.52 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, Magnesium chloride, Hepes/NaOH

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1.73638 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Jul 28, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.73638 Å / Relative weight: 1
ReflectionResolution: 1.8→40.79 Å / Num. obs: 94544 / % possible obs: 94.3 % / Redundancy: 2.14 % / CC1/2: 0.995 / Rmerge(I) obs: 0.042 / Rrim(I) all: 0.055 / Net I/σ(I): 15.37
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.8-1.910.072146670.9870.0941
1.91-2.040.058142880.990.0761
2.04-2.210.05133290.9910.0661
2.21-2.420.046124330.9920.0611
2.42-2.70.042110850.9930.0551
2.7-3.120.041101070.9930.0531
3.12-3.810.0484800.9930.0531
3.81-5.360.03766030.9940.0491
5.36-500.04235520.9930.0551

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata scaling
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→37.7 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.41 / Phase error: 18.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1931 1379 5 %
Rwork0.1411 --
obs0.1437 27591 98.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→37.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4670 0 0 354 5024
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084747
X-RAY DIFFRACTIONf_angle_d0.9796460
X-RAY DIFFRACTIONf_dihedral_angle_d6.249666
X-RAY DIFFRACTIONf_chiral_restr0.055778
X-RAY DIFFRACTIONf_plane_restr0.009833
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.280.17231350.11782556X-RAY DIFFRACTION96
2.28-2.370.22061340.1272560X-RAY DIFFRACTION98
2.37-2.480.23221370.13912593X-RAY DIFFRACTION98
2.48-2.610.19051380.14392614X-RAY DIFFRACTION98
2.61-2.770.22491360.15012597X-RAY DIFFRACTION99
2.77-2.990.2181390.16392630X-RAY DIFFRACTION99
2.99-3.290.22471390.15312651X-RAY DIFFRACTION99
3.29-3.760.19491410.14542669X-RAY DIFFRACTION100
3.76-4.740.14541400.11762660X-RAY DIFFRACTION100
4.74-37.70.17361400.14992682X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 14.1611 Å / Origin y: -1.0089 Å / Origin z: 14.2384 Å
111213212223313233
T0.0812 Å2-0.0086 Å20.0042 Å2-0.0731 Å2-0.0033 Å2--0.0773 Å2
L0.2692 °20.0119 °20.1447 °2-0.2319 °2-0.0059 °2--0.2876 °2
S-0.0336 Å °0.003 Å °-0.0075 Å °0.0332 Å °0.0142 Å °-0.0211 Å °-0.0747 Å °0.038 Å °-0.0204 Å °
Refinement TLS groupSelection details: all

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