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- PDB-8cjb: A268M variant of the CODH/ACS complex of C. hydrogenoformans -

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Basic information

Entry
Database: PDB / ID: 8cjb
TitleA268M variant of the CODH/ACS complex of C. hydrogenoformans
Components
  • CO-methylating acetyl-CoA synthase
  • Carbon monoxide dehydrogenase
KeywordsOXIDOREDUCTASE / CODH / ACS
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 / response to hydrogen peroxide ...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 / FE2/S2 (INORGANIC) CLUSTER / 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: 2.5 Å
AuthorsRuickoldt, J. / Jeoung, J. / Lennartz, F. / Dobbek, H.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)EXC 2008 390540038 Germany
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2024
Title: Coupling CO 2 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.
History
DepositionFeb 13, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 21, 2024Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 31, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.title / _citation_author.identifier_ORCID

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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)157,04612
Polymers155,5242
Non-polymers1,52310
Water4,414245
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2390 Å2
ΔGint-88 kcal/mol
Surface area52400 Å2
Unit cell
Length a, b, c (Å)142.115, 142.115, 290.244
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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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: 82351.516 Da / Num. of mol.: 1 / Mutation: A268M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Carboxydothermus hydrogenoformans Z-2901 (bacteria)
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, 255 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-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4
#6: Chemical ChemComp-OH / HYDROXIDE ION


Mass: 17.007 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: HO / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-ACT / ACETATE ION


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


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#9: 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
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 245 / 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: 2.71 Å3/Da / Density % sol: 54.66 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 4.85
Details: 1.12 uL of the reservoir solution (0.1 M sodium acetate, 210 g/L MPD, 60 g/L PEG 4000) were mixed with 0.28 uL 19.8 g/L CODH/ACS in 50 mM Mops pH 7.6, 150 mM NaCl, 1.6 mM Ti(III)-EDTA to ...Details: 1.12 uL of the reservoir solution (0.1 M sodium acetate, 210 g/L MPD, 60 g/L PEG 4000) were mixed with 0.28 uL 19.8 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 6M / Detector: PIXEL / Date: Jan 14, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.38→48.38 Å / Num. obs: 69971 / % possible obs: 99.98 % / Redundancy: 19.8 % / Rpim(I) all: 0.084 / Net I/σ(I): 9.5
Reflection shellResolution: 2.38→2.47 Å / Redundancy: 20.66 % / Num. unique obs: 6875 / CC1/2: 0.342

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→45.02 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2351 1663 1.47 %
Rwork0.2059 --
obs0.2063 60539 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→45.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10919 0 28 245 11192
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01511276
X-RAY DIFFRACTIONf_angle_d1.96215298
X-RAY DIFFRACTIONf_dihedral_angle_d23.9091544
X-RAY DIFFRACTIONf_chiral_restr0.0941695
X-RAY DIFFRACTIONf_plane_restr0.0141989
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.570.36041390.34899339X-RAY DIFFRACTION100
2.57-2.660.32121350.32889247X-RAY DIFFRACTION100
2.66-2.750.33741390.31469314X-RAY DIFFRACTION100
2.75-2.860.32641390.30389345X-RAY DIFFRACTION100
2.86-2.990.31661350.27549288X-RAY DIFFRACTION100
2.99-3.150.26211370.25839333X-RAY DIFFRACTION100
3.15-3.350.25621430.24089275X-RAY DIFFRACTION100
3.35-3.610.23831340.1979304X-RAY DIFFRACTION100
3.61-3.970.17991410.18349335X-RAY DIFFRACTION100
3.97-4.540.18511420.15069292X-RAY DIFFRACTION100
4.54-5.720.23891400.16219328X-RAY DIFFRACTION100
5.72-45.020.19091390.16119298X-RAY DIFFRACTION100
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)
10.50890.0991-0.12141.026-0.13980.59-0.0161-0.1138-0.00770.0728-0.0369-0.21410.02390.32890.07330.35180.0380.02330.50760.09680.401-34.1636-49.0906-24.0163
20.9960.3024-0.12581.13720.51561.76050.06960.11890.2965-0.0371-0.08960.4477-0.3431-0.38930.02020.32980.06540.05150.39390.10380.4383-57.7572-34.9436-27.719
31.40190.2463-0.02591.7232-0.86460.67790.0399-0.42210.0350.6037-0.05450.0841-0.14450.24910.00180.6193-0.00220.05090.54940.01170.4139-42.0275-34.302-2.1117
40.99010.1904-0.20851.28520.55272.19080.0491-0.12490.16370.12-0.0739-0.0818-0.26580.3040.00690.2918-0.02210.02020.4050.0870.3703-35.2355-27.5836-30.3261
50.8249-0.0980.04391.4526-0.08471.46870.0140.11610.0289-0.1561-0.0105-0.020.05970.1804-0.00540.372-0.0641-0.04860.38490.05030.313617.7744-58.081-14.8062
61.5061-0.39850.73870.5053-0.23351.0626-00.32090.38820.0302-0.14-0.1546-0.2960.16140.14870.4601-0.0871-0.01250.51750.11170.429512.273-37.0164-28.9837
71.2992-0.0575-0.0051.38270.33161.8437-0.02160.24880.1512-0.17690.07110.0649-0.1544-0.2388-0.03080.4951-0.0408-0.03160.55530.11210.4817-0.7148-33.139-42.3131
82.52481.1386-1.03822.4234-0.57791.9933-0.07270.26520.057-0.14510.05950.01150.0113-0.0840.00520.4526-0.0091-0.02070.38330.00950.33331.0184-65.7221-45.2771
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 127 )
2X-RAY DIFFRACTION2chain 'A' and (resid 128 through 255 )
3X-RAY DIFFRACTION3chain 'A' and (resid 256 through 408 )
4X-RAY DIFFRACTION4chain 'A' and (resid 409 through 670 )
5X-RAY DIFFRACTION5chain 'B' and (resid 5 through 286 )
6X-RAY DIFFRACTION6chain 'B' and (resid 287 through 368 )
7X-RAY DIFFRACTION7chain 'B' and (resid 369 through 496 )
8X-RAY DIFFRACTION8chain 'B' and (resid 497 through 734 )

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