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- PDB-7zkv: F231A variant of the CODH/ACS complex of C. hydrogenoformans -

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Basic information

Entry
Database: PDB / ID: 7zkv
TitleF231A variant of the CODH/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 / : / acetyl-CoA metabolic process / hydroxylamine reductase activity / 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 / : / acetyl-CoA metabolic process / hydroxylamine reductase activity / nickel cation binding / generation of precursor metabolites and energy / peroxidase activity / response to hydrogen peroxide / 4 iron, 4 sulfur cluster binding / metal ion binding
Similarity search - Function
CO dehydrogenase/acetyl-CoA synthase complex beta subunit , C-terminal / CO dehydrogenase/acetyl-CoA synthase complex beta subunit / Bifunctional carbon monoxide dehydrogenase/acetyl-coa synthase, domain 3 superfamily / Carbon monoxide dehydrogenase subunit alpha ,N-terminal / CO dehydrogenase/acetyl-CoA synthase complex beta subunit / Carbon monoxide dehydrogenase subunit alpha N-terminal domain / ACS/CODH beta subunit C-terminal / Ni-containing CO dehydrogenase / CO dehydrogenase, alpha-bundle / Hydroxylamine reductase/Ni-containing CO dehydrogenase ...CO dehydrogenase/acetyl-CoA synthase complex beta subunit , C-terminal / CO dehydrogenase/acetyl-CoA synthase complex beta subunit / Bifunctional carbon monoxide dehydrogenase/acetyl-coa synthase, domain 3 superfamily / Carbon monoxide dehydrogenase subunit alpha ,N-terminal / CO dehydrogenase/acetyl-CoA synthase complex beta subunit / Carbon monoxide dehydrogenase subunit alpha N-terminal domain / 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: 2.066 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
Citation
Journal: Angew.Chem.Int.Ed.Engl. / Year: 2024
Title: Coupling CO2 Reduction and Acetyl-CoA Formation: The Role of a CO Capturing Tunnel in Enzymatic Catalysis.
Authors: Ruickoldt, J. / Jeoung, J.H. / Rudolph, M.A. / Lennartz, F. / Kreibich, J. / Schomacker, R. / Dobbek, H.
#1: Journal: 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
Revision 1.2Jun 19, 2024Group: Database references / Category: citation / citation_author

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)157,14214
Polymers155,2072
Non-polymers1,93512
Water17,457969
1
A: Carbon monoxide dehydrogenase
hetero molecules

A: Carbon monoxide dehydrogenase
hetero molecules

B: CO-methylating acetyl-CoA synthase
hetero molecules

B: CO-methylating acetyl-CoA synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)314,28428
Polymers310,4144
Non-polymers3,87024
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_444-y-1,-x-1,-z-1/61
crystal symmetry operation5_554y,-x+y,z-1/61
crystal symmetry operation8_445x-y-1,-y-1,-z1
Buried area22520 Å2
ΔGint-293 kcal/mol
Surface area89390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)142.640, 142.640, 291.310
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
11B-1211-

HOH

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Carbon monoxide dehydrogenase


Mass: 73096.000 Da / Num. of mol.: 1 / Mutation: F231A
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 , 8 types, 981 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.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#7: 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
#8: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#9: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 969 / 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: 2.76 Å3/Da / Density % sol: 55.37 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 5
Details: To form the drops 0.7 uL of the reservoir solution (0.1 M Na-acetate pH 5, 40 g/L PEG 4000, 210 g/L MPD) were mixed with 0.7 uL of 29.6 g/L CODH/ACS solution in 50 mM Mops pH 7.6, 150 mM ...Details: To form the drops 0.7 uL of the reservoir solution (0.1 M Na-acetate pH 5, 40 g/L PEG 4000, 210 g/L MPD) were mixed with 0.7 uL of 29.6 g/L CODH/ACS solution in 50 mM Mops pH 7.6, 150 mM NaCl, 1.6 mM Ti(III)-EDTA

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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: Jun 10, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.066→48.55 Å / Num. obs: 106961 / % possible obs: 99.73 % / Redundancy: 39.82 % / CC1/2: 0.998 / Net I/σ(I): 13.4
Reflection shellResolution: 2.07→2.14 Å / Num. unique obs: 10238 / CC1/2: 0.512 / % possible all: 97.32

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7ZKJ

7zkj


Resolution: 2.066→42.382 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2144 2133 1.05 %
Rwork0.1728 200341 -
obs0.1732 106942 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 102.13 Å2 / Biso mean: 38.9564 Å2 / Biso min: 18.36 Å2
Refinement stepCycle: final / Resolution: 2.066→42.382 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10900 0 54 969 11923
Biso mean--39.34 44.13 -
Num. residues----1399
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00911278
X-RAY DIFFRACTIONf_angle_d1.05815265
X-RAY DIFFRACTIONf_chiral_restr0.0631694
X-RAY DIFFRACTIONf_plane_restr0.0061981
X-RAY DIFFRACTIONf_dihedral_angle_d9.8029436
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.0663-2.11440.3921380.31931278396
2.1144-2.16720.35531410.290613457100
2.1672-2.22580.29821390.26913393100
2.2258-2.29130.27651410.251313381100
2.2913-2.36530.22661420.223113353100
2.3653-2.44980.27111430.20713427100
2.4498-2.54790.23941430.198613432100
2.5479-2.66380.20121450.185513321100
2.6638-2.80420.25691410.175113431100
2.8042-2.97990.23931440.171813396100
2.9799-3.20990.21341430.167513401100
3.2099-3.53280.19931470.153513388100
3.5328-4.04360.21381410.135813392100
4.0436-5.09320.13831460.12813412100
5.0932-42.3820.18531390.155813374100
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)
10.59830.2164-0.19360.9275-0.16240.8631-0.0047-0.0637-0.02970.0834-0.0656-0.24770.04280.36750.06520.21960.04020.01610.36280.0980.2962-34.3068-49.2187-24.1084
20.94010.4295-0.11181.84390.79262.41320.03490.09190.30650.0129-0.08820.4169-0.3178-0.31570.07380.19670.05450.03930.25110.07880.3407-58.0664-34.9879-27.6861
32.36950.5488-0.26472.1894-0.88391.49590.0152-0.3778-0.00520.3853-0.0787-0.0837-0.09820.36630.06410.3892-0.00570.01560.40950.02110.2891-41.0719-34.4214-3.3155
40.6903-0.0239-0.34560.8750.22072.04360.0441-0.13350.10790.1554-0.0519-0.0942-0.16870.33310.01550.183-0.02910.00730.29650.06130.283-36.3934-28.0894-27.8727
50.7438-0.02420.17071.5591-0.19841.6456-0.02060.12450.0482-0.12530.008-0.07060.03730.21770.00610.1908-0.0414-0.0340.23920.03370.180717.7553-58.2498-14.8863
66.6143-2.39672.26821.4261-1.02561.7230.00490.44640.5162-0.0179-0.1608-0.2754-0.28710.1680.1540.3469-0.101-0.02050.37430.08270.298516.2228-39.7262-22.7283
71.6453-0.3326-0.09681.75320.79322.4069-0.0270.25740.2349-0.24110.0683-0.0398-0.247-0.175-0.04170.2795-0.0288-0.0190.34270.14260.3108-0.7218-32.6215-43.225
83.10431.5945-1.19062.6539-0.71742.4608-0.02060.21030.0792-0.15230.04860.00710.0005-0.056-0.02780.25110.0074-0.01360.17110.01240.17810.8936-65.8538-45.3641
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 127 )A2 - 127
2X-RAY DIFFRACTION2chain 'A' and (resid 128 through 255 )A128 - 255
3X-RAY DIFFRACTION3chain 'A' and (resid 256 through 388 )A256 - 388
4X-RAY DIFFRACTION4chain 'A' and (resid 389 through 670 )A389 - 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 496 )B347 - 496
8X-RAY DIFFRACTION8chain 'B' and (resid 497 through 734 )B497 - 734

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