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- PDB-7xdm: ChCODH2 A559W mutant in anaerobic condition -

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Basic information

Entry
Database: PDB / ID: 7xdm
TitleChCODH2 A559W mutant in anaerobic condition
ComponentsCarbon monoxide dehydrogenase 2
KeywordsOXIDOREDUCTASE / Carbon monoxide dehydrogenase / ELECTRON TRANSPORT
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 / FE(4)-NI(1)-S(5) CLUSTER / IRON/SULFUR CLUSTER / Carbon monoxide dehydrogenase 2
Similarity search - Component
Biological speciesCarboxydothermus hydrogenoformans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 Å
AuthorsHeo, Y.Y. / Kim, S.M.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2015M3D3A1A01064919 Korea, Republic Of
National Research Foundation (NRF, Korea)2020R1A5A1019631 Korea, Republic Of
CitationJournal: Nat Catal / Year: 2022
Title: O2-tolerant CO dehydrogenase via tunnel redesign for the removal of CO from industrial flue gas
Authors: Kim, S.M. / Lee, J.H. / Kang, S.H. / Heo, Y.Y. / Yoon, H.J. / Hahn, J.S. / Lee, H.H. / Kim, Y.H.
History
DepositionMar 28, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 19, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: 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
A: Carbon monoxide dehydrogenase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,2774
Polymers69,3071
Non-polymers9703
Water7,512417
1
A: Carbon monoxide dehydrogenase 2
hetero molecules

A: Carbon monoxide dehydrogenase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,5548
Polymers138,6142
Non-polymers1,9406
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area9370 Å2
ΔGint-175 kcal/mol
Surface area37620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.483, 75.803, 71.384
Angle α, β, γ (deg.)90.000, 111.480, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1120-

HOH

21A-1217-

HOH

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Components

#1: Protein Carbon monoxide dehydrogenase 2 / CODH 2


Mass: 69307.023 Da / Num. of mol.: 1 / Mutation: A559W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Carboxydothermus hydrogenoformans (bacteria)
Strain: ATCC BAA-161 / DSM 6008 / Z-2901 / Gene: cooS2, cooSII, CHY_0085 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9F8A8, anaerobic carbon monoxide dehydrogenase
#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-NFS / FE(4)-NI(1)-S(5) CLUSTER


Mass: 442.398 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4NiS5 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 417 / 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: 2.02 Å3/Da / Density % sol: 39.26 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M HEPES/NaOH pH 7.5, 200 mM MgCl2, 25% (w/v) polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.9794 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 18, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.74→50 Å / Num. obs: 56045 / % possible obs: 98.4 % / Redundancy: 6.9 % / Biso Wilson estimate: 20.75 Å2 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.029 / Rrim(I) all: 0.077 / Χ2: 0.595 / Net I/σ(I): 5.1 / Num. measured all: 384668
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.74-1.776.60.58827810.8840.2430.6370.50898.4
1.77-1.86.50.50827740.9130.2130.5520.47598.2
1.8-1.846.30.43827330.9270.1870.4770.46196.9
1.84-1.877.10.38228390.9510.1530.4120.50499.3
1.87-1.927.10.30927980.9650.1240.3330.52599.4
1.92-1.967.10.27827910.9710.1120.30.52198.6
1.96-2.0170.23528130.9780.0950.2540.5499
2.01-2.066.90.21527750.980.0870.2330.56298.5
2.06-2.126.80.17328180.9860.0710.1870.56998.5
2.12-2.196.30.14727550.9870.0630.1610.58196.7
2.19-2.277.10.12327900.9940.0490.1330.58498.9
2.27-2.367.10.11128340.9940.0440.1190.62399.2
2.36-2.477.10.09928170.9940.040.1070.65399
2.47-2.67.10.08528040.9960.0340.0910.62698.2
2.6-2.766.80.07527690.9960.0310.0810.66598
2.76-2.986.80.06627800.9970.0270.0710.67797.5
2.98-3.277.20.05528570.9980.0220.0590.68399.5
3.27-3.7570.04828350.9980.0190.0510.798.5
3.75-4.726.70.0427900.9990.0160.0430.67897.5
4.72-506.80.0428920.9990.0160.0440.73698.7

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1SU7

1su7


Resolution: 1.74→40.83 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1915 2843 5.08 %
Rwork0.1644 53140 -
obs0.1658 55983 97.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 73.25 Å2 / Biso mean: 27.6013 Å2 / Biso min: 11.74 Å2
Refinement stepCycle: final / Resolution: 1.74→40.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4662 0 22 417 5101
Biso mean--26.41 35.24 -
Num. residues----633
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.74-1.770.28611410.23062451259292
1.77-1.80.24641390.21792662280198
1.8-1.830.21761310.20762617274897
1.83-1.870.23581570.20322678283599
1.87-1.910.22111420.19062664280699
1.91-1.960.2141440.1852661280599
1.96-20.21661370.17532684282199
2-2.060.25961310.18012651278299
2.06-2.120.20581490.16942672282198
2.12-2.190.21271400.1642622276297
2.19-2.270.20371500.15492661281199
2.27-2.360.17141560.15912668282499
2.36-2.460.1711530.15152674282799
2.46-2.590.17891350.15452683281898
2.59-2.760.19921340.1592650278498
2.76-2.970.17011410.16352643278497
2.97-3.270.19771410.15962717285899
3.27-3.740.17781600.15432693285398
3.74-4.710.1351300.14052658278897
4.71-40.830.21421320.17452731286397

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