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

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Basic information

Entry
Database: PDB / ID: 7xdn
TitleTunnel-redesigned O2-tolerant CO dehydrogenase for removal of CO in real flue gas (ChCODH2 A559H 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: 1.8 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)70,2294
Polymers69,2591
Non-polymers9703
Water9,026501
1
A: Carbon monoxide dehydrogenase 2
hetero molecules

A: Carbon monoxide dehydrogenase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,4588
Polymers138,5182
Non-polymers1,9406
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area9370 Å2
ΔGint-177 kcal/mol
Surface area37610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.859, 76.026, 71.613
Angle α, β, γ (deg.)90.000, 111.590, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1070-

HOH

21A-1151-

HOH

31A-1206-

HOH

41A-1300-

HOH

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Components

#1: Protein Carbon monoxide dehydrogenase 2 / CODH 2


Mass: 69258.961 Da / Num. of mol.: 1 / Mutation: A559H
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.: 501 / 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: 2.04 Å3/Da / Density % sol: 39.83 %
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: 1.8→50 Å / Num. obs: 51563 / % possible obs: 99.9 % / Redundancy: 6.8 % / Biso Wilson estimate: 19.26 Å2 / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.038 / Rrim(I) all: 0.099 / Χ2: 0.602 / Net I/σ(I): 5.7 / Num. measured all: 352221
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.8-1.836.60.64726110.8620.2670.70.377100
1.83-1.866.80.5625630.9050.2280.6060.385100
1.86-1.96.90.46325320.9220.1870.50.402100
1.9-1.946.90.4225920.9370.1690.4540.401100
1.94-1.9870.36925630.9470.1480.3980.415100
1.98-2.0370.31925340.9640.1280.3440.425100
2.03-2.086.90.29625790.9660.120.320.426100
2.08-2.136.90.22925650.9760.0930.2480.454100
2.13-2.26.80.19725760.9830.0810.2130.464100
2.2-2.276.60.16625940.9870.070.180.484100
2.27-2.356.10.14425710.9870.0640.1580.504100
2.35-2.446.50.12525590.9910.0530.1360.527100
2.44-2.556.90.10626030.9940.0430.1140.55100
2.55-2.697.30.09525580.9950.0370.1020.60499.9
2.69-2.867.20.08125670.9960.0320.0880.63499.8
2.86-3.087.20.0726090.9970.0280.0760.71399.8
3.08-3.397.10.05825800.9980.0230.0620.80699.7
3.39-3.886.80.04925710.9980.020.0530.97699.7
3.88-4.8860.04325970.9970.020.0481.07499.3
4.88-507.20.04826390.9970.0190.0521.37299.4

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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: 1.8→35.19 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 19.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1997 2660 5.16 %
Rwork0.1643 48896 -
obs0.1661 51556 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 78.33 Å2 / Biso mean: 25.4175 Å2 / Biso min: 9.74 Å2
Refinement stepCycle: final / Resolution: 1.8→35.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4658 0 22 501 5181
Biso mean--27.23 32.53 -
Num. residues----633
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.830.22761480.19942547269599
1.83-1.870.26381430.199525802723100
1.87-1.910.25361370.195225372674100
1.91-1.950.23161370.192625682705100
1.95-1.990.22491410.181825682709100
1.99-2.040.23091490.180625652714100
2.04-2.10.18691260.173325632689100
2.1-2.160.21321420.170325732715100
2.16-2.230.21761220.162625742696100
2.23-2.310.21421040.174226042708100
2.31-2.40.20731500.167425682718100
2.4-2.510.22221180.168126072725100
2.51-2.640.22291420.169925642706100
2.64-2.810.19351510.167225762727100
2.81-3.030.20541420.170125572699100
3.03-3.330.19661410.160725782719100
3.33-3.810.15391540.148225762730100
3.81-4.80.19491520.13052570272299
4.8-35.190.1811610.16832621278299

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