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

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Basic information

Entry
Database: PDB / ID: 7err
TitleTunnel-redesigned O2-tolerant CO dehydrogenase for removal of CO in real flue gas (Aerobic ChCODH2 A559W mutant)
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 Z-2901 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.26 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
DepositionMay 6, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 5, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Nov 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

Downloads & links

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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
Water4,071226
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 area8480 Å2
ΔGint-120 kcal/mol
Surface area37400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.144, 75.137, 70.785
Angle α, β, γ (deg.)90.000, 111.200, 90.000
Int Tables number5
Space group name H-MC121

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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 Z-2901 (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.: 226 / 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: 38.68 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M HEPES/NaOH pH 7.0, 50 mM MgCl2, 25 % (w/v) polyethyleneglycol 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: Oct 21, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.26→50 Å / Num. obs: 25635 / % possible obs: 99.4 % / Redundancy: 3.4 % / Biso Wilson estimate: 32.26 Å2 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.063 / Rrim(I) all: 0.118 / Χ2: 0.681 / Net I/σ(I): 5.5 / Num. measured all: 86418
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.26-2.33.10.51312130.8060.3310.6120.595.2
2.3-2.343.20.4912830.8150.3180.5860.49697.8
2.34-2.393.20.41912350.880.2710.5010.49998.7
2.39-2.433.30.41912870.8370.2680.4980.49599.8
2.43-2.493.30.35412830.8910.2280.4220.47599.6
2.49-2.553.30.32812740.910.2140.3930.599.8
2.55-2.6130.2812860.9130.1940.3420.486100
2.61-2.683.20.25312800.9230.1690.3050.5299.9
2.68-2.763.20.22712610.9340.1490.2730.51499.9
2.76-2.853.40.20512970.9550.1290.2420.527100
2.85-2.953.60.18913010.9660.1140.2210.54799.8
2.95-3.073.60.14712800.9830.0890.1720.545100
3.07-3.213.60.12712880.9830.0780.1490.597100
3.21-3.383.60.10412970.9880.0640.1220.62599.9
3.38-3.593.60.08312760.9920.0510.0980.71999.8
3.59-3.863.50.06612790.9940.0410.0780.78999.8
3.86-4.253.50.05512870.9950.0340.0650.97599.5
4.25-4.873.10.05112990.9940.0340.0611.09799.5
4.87-6.133.30.0513040.9940.0330.061.01899.8
6.13-503.70.04413250.9970.0270.0521.51799.5

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Processing

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

1su7


Resolution: 2.26→40.72 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 17.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1976 1235 4.82 %RANDOM
Rwork0.1443 24397 --
obs0.1468 25632 99.33 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 135.07 Å2 / Biso mean: 35.9194 Å2 / Biso min: 17.7 Å2
Refinement stepCycle: final / Resolution: 2.26→40.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4619 0 22 226 4867
Biso mean--48.1 38.07 -
Num. residues----633
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.26-2.350.21941410.1492603274496
2.35-2.460.21491420.13932667280999
2.46-2.590.23261210.132327522873100
2.59-2.750.20361320.137827002832100
2.75-2.960.22391230.154527302853100
2.96-3.260.20881330.159127302863100
3.26-3.730.18491670.145427092876100
3.73-4.70.17391320.12927282860100
4.7-40.720.19391440.15227782922100

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