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- PDB-8omx: NI,FE-CODH -600mV state : 1 min Dioxygen Exposure -

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Basic information

Entry
Database: PDB / ID: 8omx
TitleNI,FE-CODH -600mV state : 1 min Dioxygen Exposure
ComponentsCarbon monoxide dehydrogenase 2
KeywordsOXIDOREDUCTASE / CLUSTER C / 4FE-4S / CYTOPLASM / IRON / IRON-SULFUR / MEMBRANE / METAL-BINDING / NICKEL
Function / homology
Function and homology information


anaerobic carbon monoxide dehydrogenase / anaerobic carbon-monoxide dehydrogenase activity / : / hydroxylamine reductase 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 / HYDROSULFURIC ACID / 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: 1.5 Å
AuthorsBasak, Y. / Jeoung, J.-H. / Dobbek, H.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)DO 785/6-2 Germany
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2023
Title: Stepwise O 2 -Induced Rearrangement and Disassembly of the [NiFe 4 (OH)( mu 3 -S) 4 ] Active Site Cluster of CO Dehydrogenase.
Authors: Basak, Y. / Jeoung, J.H. / Domnik, L. / Dobbek, H.
History
DepositionMar 31, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 6, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
X: Carbon monoxide dehydrogenase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,0526
Polymers66,9921
Non-polymers1,0605
Water10,287571
1
X: Carbon monoxide dehydrogenase 2
hetero molecules

X: Carbon monoxide dehydrogenase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,10512
Polymers133,9852
Non-polymers2,12010
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_757-x+2,y,-z+21
Buried area9740 Å2
ΔGint-208 kcal/mol
Surface area37850 Å2
Unit cell
Length a, b, c (Å)112.740, 75.501, 71.503
Angle α, β, γ (deg.)90.00, 111.77, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11X-1504-

HOH

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Components

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Protein , 1 types, 1 molecules X

#1: Protein Carbon monoxide dehydrogenase 2 / CODH 2


Mass: 66992.477 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Carboxydothermus hydrogenoformans Z-2901 (bacteria)
Strain: Z-2901 / DSM 6008 / Gene: cooS2, cooSII, CHY_0085 / Plasmid: pET28A / Production host: Escherichia coli B (bacteria) / Strain (production host): ROSSETTA DE3
References: UniProt: Q9F8A8, anaerobic carbon monoxide dehydrogenase

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Non-polymers , 6 types, 576 molecules

#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: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-H2S / HYDROSULFURIC ACID / HYDROGEN SULFIDE


Mass: 34.081 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2S / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 571 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.11 Å3/Da / Density % sol: 41.7 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M Bis-Tris pH 6.5, PEG 3350 10-18%, Ammonium sulphate 0.18M

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.5→40.85 Å / Num. obs: 83154 / % possible obs: 94 % / Redundancy: 3.38 % / CC1/2: 0.999 / Net I/σ(I): 0.115
Reflection shellResolution: 1.5→1.56 Å / Num. unique obs: 7758 / CC1/2: 0.658

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→40.82 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1928 2100 2.53 %
Rwork0.1554 --
obs0.1564 83024 93.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.5→40.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4654 0 23 571 5248
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114897
X-RAY DIFFRACTIONf_angle_d1.0916705
X-RAY DIFFRACTIONf_dihedral_angle_d19.5571835
X-RAY DIFFRACTIONf_chiral_restr1.454808
X-RAY DIFFRACTIONf_plane_restr0.01869
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.540.33251230.30824762X-RAY DIFFRACTION83
1.54-1.580.25051400.26315376X-RAY DIFFRACTION93
1.58-1.620.24171400.23325394X-RAY DIFFRACTION95
1.62-1.670.23931410.20725429X-RAY DIFFRACTION95
1.67-1.720.21141410.19585444X-RAY DIFFRACTION95
1.72-1.780.25261430.16935524X-RAY DIFFRACTION96
1.78-1.850.1981420.16055459X-RAY DIFFRACTION96
1.85-1.940.19431360.15835257X-RAY DIFFRACTION91
1.94-2.040.19031420.14835485X-RAY DIFFRACTION96
2.04-2.170.20721450.14825549X-RAY DIFFRACTION96
2.17-2.330.1811410.1485447X-RAY DIFFRACTION95
2.33-2.570.1921400.15635412X-RAY DIFFRACTION94
2.57-2.940.18551360.15545244X-RAY DIFFRACTION91
2.94-3.710.18391440.1435557X-RAY DIFFRACTION96
3.71-40.820.16361460.12645585X-RAY DIFFRACTION95
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.36060.01620.33870.3533-0.0930.39970.0879-0.0095-0.11950.0492-0.0331-0.06380.08920.02980.00230.1270.00320.00470.15330.01420.178391.827-7.777274.9417
20.5196-0.2639-0.07940.58950.10880.6908-0.09130.00190.20160.02460.0047-0.0108-0.29780.0444-0.03330.2417-0.0181-0.04060.1278-0.00890.210194.131527.915176.7531
30.31910.05910.22950.509-0.0460.2137-0.09090.09420.0827-0.08480.0067-0.0622-0.17210.0714-0.0050.1709-0.0389-0.00270.16030.01470.164297.552820.294464.7564
40.53210.3044-0.05560.21890.00450.2901-0.0145-0.11940.10480.333-0.01960.0156-0.1349-0.1517-0.02830.3226-0.001-0.01450.167-0.01370.120593.749616.1624100.3532
50.53730.25750.21830.7976-0.00050.3652-0.0297-0.11860.08740.25310.01150.0678-0.1574-0.0848-00.28530.01140.01350.2046-0.00810.168786.728711.523293.5956
60.41170.1131-0.14550.8862-0.26480.33420.0483-0.0959-0.09260.2003-0.0876-0.1878-0.08330.0960.00470.1958-0.0521-0.05110.20170.0350.2014114.081710.803888.3206
70.4860.14450.03620.67710.02430.27630.00210.0114-0.05870.0406-0.0167-0.1502-0.06550.0998-0.00070.1183-0.03520.00280.18040.0090.1822111.39359.569172.2568
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'X' and (resid 4 through 73 )
2X-RAY DIFFRACTION2chain 'X' and (resid 74 through 154 )
3X-RAY DIFFRACTION3chain 'X' and (resid 155 through 234 )
4X-RAY DIFFRACTION4chain 'X' and (resid 235 through 293 )
5X-RAY DIFFRACTION5chain 'X' and (resid 294 through 389 )
6X-RAY DIFFRACTION6chain 'X' and (resid 390 through 511 )
7X-RAY DIFFRACTION7chain 'X' and (resid 512 through 636 )

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