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- PDB-7zkj: CODH/ACS complex of C. hydrogenoformans -

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Basic information

Entry
Database: PDB / ID: 7zkj
TitleCODH/ACS complex of C. hydrogenoformans
Components
  • CO-methylating acetyl-CoA synthase
  • Carbon monoxide dehydrogenase
KeywordsOXIDOREDUCTASE / CO2 reduction / acetyl-CoA synthesis / carbon monoxide
Function / homology
Function and homology information


CO-methylating acetyl-CoA synthase / CO-methylating acetyl-CoA synthase activity / anaerobic carbon monoxide dehydrogenase / anaerobic carbon-monoxide dehydrogenase activity / : / hydroxylamine reductase activity / acetyl-CoA metabolic process / nickel cation binding / generation of precursor metabolites and energy / peroxidase activity ...CO-methylating acetyl-CoA synthase / CO-methylating acetyl-CoA synthase activity / anaerobic carbon monoxide dehydrogenase / anaerobic carbon-monoxide dehydrogenase activity / : / hydroxylamine reductase activity / acetyl-CoA metabolic process / nickel cation binding / generation of precursor metabolites and energy / peroxidase activity / response to hydrogen peroxide / 2 iron, 2 sulfur cluster binding / 4 iron, 4 sulfur cluster binding / metal ion binding
Similarity search - Function
Carbon monoxide dehydrogenase subunit alpha ,N-terminal / Carbon monoxide dehydrogenase subunit alpha N-terminal domain / CO dehydrogenase/acetyl-CoA synthase complex beta subunit / Bifunctional carbon monoxide dehydrogenase/acetyl-coa synthase, domain 3 superfamily / CO dehydrogenase/acetyl-CoA synthase complex beta subunit , C-terminal / CO dehydrogenase/acetyl-CoA synthase complex beta subunit / ACS/CODH beta subunit C-terminal / Ni-containing CO dehydrogenase / CO dehydrogenase, alpha-bundle / Hydroxylamine reductase/Ni-containing CO dehydrogenase ...Carbon monoxide dehydrogenase subunit alpha ,N-terminal / Carbon monoxide dehydrogenase subunit alpha N-terminal domain / CO dehydrogenase/acetyl-CoA synthase complex beta subunit / Bifunctional carbon monoxide dehydrogenase/acetyl-coa synthase, domain 3 superfamily / CO dehydrogenase/acetyl-CoA synthase complex beta subunit , C-terminal / CO dehydrogenase/acetyl-CoA synthase complex beta subunit / ACS/CODH beta subunit C-terminal / 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
ACETATE ION / NICKEL (II) ION / HYDROXIDE ION / Fe(3)-Ni(1)-S(4) cluster / IRON/SULFUR CLUSTER / Carbon monoxide dehydrogenase / CO-methylating acetyl-CoA synthase
Similarity search - Component
Biological speciesCarboxydothermus hydrogenoformans Z-2901 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04 Å
AuthorsRuickoldt, J. / Jeoung, J.-H. / Basak, Y. / Domnik, L. / Dobbek, H.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)EXC 2008/1 390540038 Germany
CitationJournal: ACS Catal. / Year: 2022
Title: On the Kinetics of CO2 Reduction by Ni, Fe-CO Dehydrogenases
Authors: Ruickoldt, J. / Basak, Y. / Domnik, L. / Jeoung, J.H. / Dobbek, H.
History
DepositionApr 13, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 2, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: 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
B: CO-methylating acetyl-CoA synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,39517
Polymers155,2832
Non-polymers2,11215
Water15,907883
1
B: CO-methylating acetyl-CoA synthase
hetero molecules

B: CO-methylating acetyl-CoA synthase
hetero molecules

A: Carbon monoxide dehydrogenase
hetero molecules

A: Carbon monoxide dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)314,79134
Polymers310,5674
Non-polymers4,22430
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_545x,x-y-1,-z+1/61
crystal symmetry operation6_555x-y,x,z+1/61
crystal symmetry operation8_545x-y,-y-1,-z1
Buried area23280 Å2
ΔGint-314 kcal/mol
Surface area88330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.586, 141.586, 290.124
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-1075-

HOH

21A-1170-

HOH

31B-931-

HOH

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Carbon monoxide dehydrogenase


Mass: 73172.102 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Carboxydothermus hydrogenoformans Z-2901 (bacteria)
Gene: ciss_06270 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A1L8D0M5, anaerobic carbon monoxide dehydrogenase
#2: Protein CO-methylating acetyl-CoA synthase


Mass: 82111.172 Da / Num. of mol.: 1
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: acsB, CHY_1222 / Production host: Escherichia coli (E. coli)
References: UniProt: Q3ACS4, CO-methylating acetyl-CoA synthase

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Non-polymers , 9 types, 898 molecules

#3: Chemical ChemComp-RQM / Fe(3)-Ni(1)-S(4) cluster


Mass: 410.333 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4NiS4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-OH / HYDROXIDE ION


Mass: 17.007 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: HO
#6: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#7: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#8: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#10: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 883 / 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: 2.7 Å3/Da / Density % sol: 54.5 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 4.85
Details: 0.7 uL of the reservoir solution (0.1 M sodium acetate, 210 g/L MPD, 60 g/L PEG 4000) were mixed with 0.7 uL 19.6 g/L CODH/ACS in 50 mM Mops pH 7.6, 150 mM NaCl, 1.6 mM Ti(III)-EDTA to form ...Details: 0.7 uL of the reservoir solution (0.1 M sodium acetate, 210 g/L MPD, 60 g/L PEG 4000) were mixed with 0.7 uL 19.6 g/L CODH/ACS in 50 mM Mops pH 7.6, 150 mM NaCl, 1.6 mM Ti(III)-EDTA to form the sitting drop. Crystallization was performed in an anoxic glove box.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 22, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.93→48.35 Å / Num. obs: 129067 / % possible obs: 99.84 % / Redundancy: 19.8 % / CC1/2: 0.999 / Net I/σ(I): 10.2
Reflection shellResolution: 1.93→2 Å / Num. unique obs: 12539 / CC1/2: 0.316 / % possible all: 98.55

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1aoa

1aoa


Resolution: 2.04→48.35 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 22.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1987 2181 1.05 %
Rwork0.1744 204863 -
obs0.1746 109315 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 108.84 Å2 / Biso mean: 41.2908 Å2 / Biso min: 20.51 Å2
Refinement stepCycle: final / Resolution: 2.04→48.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10906 0 66 883 11855
Biso mean--48.81 45.54 -
Num. residues----1399
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 16 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.04-2.080.35981340.32931284712981
2.08-2.130.33721390.30581276712906
2.13-2.190.3531350.28411279112926
2.19-2.250.2881390.26391283312972
2.25-2.310.26011360.25511276212898
2.31-2.390.27621370.22581283012967
2.39-2.470.2631340.21931277212906
2.47-2.570.25821350.20771281012945
2.57-2.690.28021330.19311281912952
2.69-2.830.17251400.17681282312963
2.83-3.010.21641350.17321275712892
3.01-3.240.20641340.15751281012944
3.24-3.560.15241360.14951281812954
3.56-4.080.15081360.1311282912965
4.08-5.140.14061360.12781280612942
5.14-48.350.17051420.1571278912931
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)
10.61330.0895-0.2860.7912-0.11631.0267-0.0199-0.1121-0.02530.1335-0.0406-0.2117-0.00660.36760.06080.2708-0.00120.0010.35990.07310.3217-34.3361-48.6463-23.849
21.08480.4037-0.22691.16070.5162.13570.0420.09310.2740.024-0.05010.2865-0.324-0.25470.01980.25890.02510.02530.25750.07210.3318-57.538-34.7487-27.7955
31.63280.3913-0.23091.7481-0.86431.15680.0695-0.40520.04640.3634-0.0767-0.0197-0.18840.27280.00750.4561-0.02220.0020.41880.00010.3118-41.8023-34.0971-1.7494
40.96620.032-0.39251.22260.49262.14080.0488-0.13490.15860.1622-0.0377-0.1198-0.2350.2963-0.01350.2363-0.03780.00570.28690.0430.2976-35.1287-27.1382-30.659
50.6705-0.05770.09391.1979-0.16231.5442-0.02990.10530.029-0.10520.0285-0.03010.02370.1174-0.00180.224-0.037-0.02420.23730.01720.220317.6328-57.7576-14.8478
64.7047-1.62271.29891.049-0.71411.25880.05010.40180.3773-0.0179-0.1201-0.1687-0.26060.09890.08230.3964-0.0814-0.01510.41170.04690.321616.4294-39.3459-22.4969
71.5808-0.28820.00191.67410.60171.982-0.03340.28410.2182-0.21720.0037-0.0535-0.2437-0.06520.02110.369-0.0359-0.03810.41320.11890.3465-0.8403-32.3173-43.2414
81.39390.5268-0.26462.208-0.2092.0019-0.05630.16950.0193-0.30180.0519-0.2685-0.01520.19910.00280.2789-0.03790.0180.25670.00450.24499.1774-62.6951-49.3022
93.17510.8113-0.1651.29580.37941.88690.02710.11850.11910.0567-0.03230.167-0.028-0.17250.00320.3116-0.02380.00920.23840.01530.2622-8.2029-68.2601-40.7316
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 128 )A2 - 128
2X-RAY DIFFRACTION2chain 'A' and (resid 129 through 255 )A129 - 255
3X-RAY DIFFRACTION3chain 'A' and (resid 256 through 410 )A256 - 410
4X-RAY DIFFRACTION4chain 'A' and (resid 411 through 670 )A411 - 670
5X-RAY DIFFRACTION5chain 'B' and (resid 5 through 286 )B5 - 286
6X-RAY DIFFRACTION6chain 'B' and (resid 287 through 346 )B287 - 346
7X-RAY DIFFRACTION7chain 'B' and (resid 347 through 497 )B347 - 497
8X-RAY DIFFRACTION8chain 'B' and (resid 498 through 618 )B498 - 618
9X-RAY DIFFRACTION9chain 'B' and (resid 619 through 734 )B619 - 734

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