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- PDB-8x9e: Crystal structure of CO dehydrogenase mutant with increased affin... -

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Basic information

Entry
Database: PDB / ID: 8x9e
TitleCrystal structure of CO dehydrogenase mutant with increased affinity for electron mediators in low PEG concentration
ComponentsCarbon monoxide dehydrogenase 2
KeywordsELECTRON TRANSPORT / OXIDOREDUCTASE
Function / homology
Function and homology information


anaerobic carbon monoxide dehydrogenase / carbon-monoxide dehydrogenase (ferredoxin) activity / carbon-monoxide dehydrogenase (acceptor) activity / nickel cation binding / generation of precursor metabolites and energy / 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: 2.5 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)70,1186
Polymers69,0631
Non-polymers1,0565
Water2,144119
1
A: Carbon monoxide dehydrogenase 2
hetero molecules

A: Carbon monoxide dehydrogenase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,23712
Polymers138,1262
Non-polymers2,11110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation1
MethodPISA
Unit cell
Length a, b, c (Å)112.083, 75.088, 71.140
Angle α, β, γ (deg.)90.00, 111.39, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-705-

EDO

21A-894-

HOH

31A-901-

HOH

41A-918-

HOH

51A-919-

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: 69062.789 Da / Num. of mol.: 1 / Mutation: R57G, N59L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Carboxydothermus hydrogenoformans Z-2901 (bacteria)
Gene: cooS2 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9F8A8, anaerobic carbon monoxide dehydrogenase

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Non-polymers , 6 types, 124 molecules

#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / 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 / Iron–sulfur 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 / Iron


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 119 / 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: 2.01 Å3/Da / Density % sol: 38.92 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 0.1 M HEPES/NaOH pH 7.5, 200 mM MgCl2, and 25% (w/v) PEG 3,350.

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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: Dec 20, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 18938 / % possible obs: 99.3 % / Redundancy: 3.8 % / CC1/2: 0.995 / CC star: 0.999 / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.058 / Rrim(I) all: 0.115 / Χ2: 0.443 / Net I/σ(I): 4.3 / Num. measured all: 71132
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.5-2.543.40.4748840.8130.9470.2850.5560.41392.8
2.54-2.593.40.4379160.8630.9630.2610.5120.41896
2.59-2.643.50.3959330.8530.9590.2350.4610.43398.9
2.64-2.693.70.3889340.850.9590.2290.4530.4398.6
2.69-2.753.80.3799220.8990.9730.2220.440.41999.6
2.75-2.823.80.3399620.9030.9740.1980.3940.44799.9
2.82-2.893.80.3429260.8810.9680.2010.3970.43799.9
2.89-2.963.70.2879580.9140.9770.1720.3360.45599.9
2.96-3.053.50.239550.9490.9870.1460.2730.442100
3.05-3.153.40.1889510.9560.9890.1190.2230.433100
3.15-3.263.80.1559580.9770.9940.0930.1810.44100
3.26-3.394.10.1469490.9780.9940.0840.1690.427100
3.39-3.554.10.1079600.9890.9970.0610.1230.445100
3.55-3.7340.0889610.9930.9980.0510.1020.46100
3.73-3.9740.0719410.9940.9980.0410.0820.439100
3.97-4.273.90.0549530.9960.9990.0310.0620.426100
4.27-4.73.90.0479580.9970.9990.0270.0540.431100
4.7-5.383.70.0459580.9970.9990.0270.0520.426100
5.38-6.783.40.0479710.9960.9990.030.0560.449100
6.78-5040.0329880.99910.0190.0370.55899.7

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-2000data scaling
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→35.22 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2269 968 5.16 %
Rwork0.1766 --
obs0.1791 18765 98.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→35.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4646 0 26 119 4791
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014767
X-RAY DIFFRACTIONf_angle_d1.1456492
X-RAY DIFFRACTIONf_dihedral_angle_d6.653671
X-RAY DIFFRACTIONf_chiral_restr0.058781
X-RAY DIFFRACTIONf_plane_restr0.009837
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.630.28421400.2242349X-RAY DIFFRACTION92
2.63-2.80.27521210.2212552X-RAY DIFFRACTION98
2.8-3.010.24681310.21112529X-RAY DIFFRACTION99
3.01-3.320.25941560.19292544X-RAY DIFFRACTION99
3.32-3.80.22511400.17132575X-RAY DIFFRACTION100
3.8-4.780.19191450.13992606X-RAY DIFFRACTION100
4.78-35.220.20721350.16752642X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 13.9508 Å / Origin y: -0.7721 Å / Origin z: 14.503 Å
111213212223313233
T0.2341 Å2-0.0134 Å20.0062 Å2-0.2301 Å20.0042 Å2--0.2204 Å2
L0.4685 °2-0.0192 °20.1939 °2-0.4637 °2-0.1341 °2--0.2439 °2
S-0.039 Å °-0.0378 Å °-0.0307 Å °0.0749 Å °-0.0118 Å °-0.0482 Å °-0.0834 Å °0.0177 Å °-0.0001 Å °
Refinement TLS groupSelection details: all

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