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- PDB-7xdp: Tunnel-redesigned O2-tolerant CO dehydrogenase for removal of CO ... -

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Basic information

Entry
Database: PDB / ID: 7xdp
TitleTunnel-redesigned O2-tolerant CO dehydrogenase for removal of CO in real flue gas (ChCODH2 A559S 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: 1.84 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)70,1784
Polymers69,2081
Non-polymers9703
Water10,683593
1
A: Carbon monoxide dehydrogenase 2
hetero molecules

A: Carbon monoxide dehydrogenase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,3558
Polymers138,4162
Non-polymers1,9406
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area9340 Å2
ΔGint-175 kcal/mol
Surface area38100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.934, 74.969, 71.323
Angle α, β, γ (deg.)90.000, 111.290, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1192-

HOH

21A-1366-

HOH

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Components

#1: Protein Carbon monoxide dehydrogenase 2 / CODH 2


Mass: 69207.891 Da / Num. of mol.: 1 / Mutation: A559S
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.: 593 / 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: 2.01 Å3/Da / Density % sol: 38.94 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, hanging drop
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: 5C (4A) / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 21, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.84→50 Å / Num. obs: 47693 / % possible obs: 99.9 % / Redundancy: 6.8 % / Biso Wilson estimate: 17.89 Å2 / Rmerge(I) obs: 0.103 / Rpim(I) all: 0.043 / Rrim(I) all: 0.112 / Χ2: 0.697 / Net I/σ(I): 5.4 / Num. measured all: 325933
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.84-1.8770.53823910.8960.2190.5810.374100
1.87-1.9170.46523410.9150.190.5030.398100
1.91-1.946.90.43223730.9230.1770.4680.423100
1.94-1.986.90.36124020.9390.1470.390.408100
1.98-2.036.80.32323520.9560.1330.350.418100
2.03-2.076.70.30123730.9590.1250.3270.442100
2.07-2.126.60.24723860.9670.1040.2680.454100
2.12-2.186.10.20823680.9730.0920.2280.463100
2.18-2.256.40.18524120.9810.0790.2020.506100
2.25-2.326.40.16923490.9820.0720.1840.54999.9
2.32-2.47.10.14224000.9890.0570.1530.548100
2.4-2.57.30.12823670.9910.0510.1370.56699.9
2.5-2.617.20.11523840.9930.0460.1240.61399.9
2.61-2.757.20.10223740.9940.0410.110.6699.9
2.75-2.927.10.09324050.9940.0380.1010.731100
2.92-3.157.10.0823760.9950.0320.0870.81599.8
3.15-3.466.90.0723730.9960.0290.0750.97399.8
3.46-3.966.20.06124350.9960.0270.0671.28799.8
3.96-4.996.50.05723710.9960.0250.0631.54699.3
4.99-507.40.0624610.9970.0240.0651.71599.7

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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: 1.84→33.23 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 17.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.193 2369 4.97 %
Rwork0.1484 45319 -
obs0.1506 47688 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 72.54 Å2 / Biso mean: 21.4963 Å2 / Biso min: 8.12 Å2
Refinement stepCycle: final / Resolution: 1.84→33.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4654 0 22 593 5269
Biso mean--32.65 31.15 -
Num. residues----633
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.84-1.880.24361670.20932611277898
1.88-1.920.21291190.175126732792100
1.92-1.960.20781570.166226192776100
1.96-2.010.18481200.155326582778100
2.01-2.070.23781360.155126592795100
2.07-2.130.1911380.155426752813100
2.13-2.20.20691430.1526492792100
2.2-2.270.19311520.148426662818100
2.27-2.360.21021520.147326142766100
2.36-2.470.19811310.143826962827100
2.47-2.60.18551280.144926752803100
2.6-2.770.18881320.146926532785100
2.77-2.980.23381460.154326712817100
2.98-3.280.17911480.145226832831100
3.28-3.750.16341210.133827042825100
3.75-4.730.15681220.12232687280999
4.73-33.230.19831570.16527262883100

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