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- PDB-8cja: A225L/F231A variant of the CODH/ACS complex of C. hydrogenoformans -

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Basic information

Entry
Database: PDB / ID: 8cja
TitleA225L/F231A 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 / 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: 2.1 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)158,25313
Polymers156,3412
Non-polymers1,91211
Water13,385743
1
A: Carbon monoxide dehydrogenase
B: CO-methylating acetyl-CoA synthase
hetero molecules

A: Carbon monoxide dehydrogenase
B: CO-methylating acetyl-CoA synthase
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)484,05036
Polymers479,1706
Non-polymers4,88030
Water1086
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 area22120 Å2
ΔGint-322 kcal/mol
Surface area89520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)142.219, 142.219, 290.773
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11B-944-

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: 83244.516 Da / Num. of mol.: 1 / Mutation: A225L
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 , 7 types, 754 molecules

#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: 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
#5: 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
#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-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni / Feature type: SUBJECT OF INVESTIGATION
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 743 / 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: 54.54 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 1.12 uL of the reservoir solution (0.1 M sodium acetate, 250 g/L MPD, 40 g/L PEG 4000) were mixed with 0.28 uL 23.7 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, 250 g/L MPD, 40 g/L PEG 4000) were mixed with 0.28 uL 23.7 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: Jun 9, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.91→48.46 Å / Num. obs: 134637 / % possible obs: 99.89 % / Redundancy: 19.8 % / CC1/2: 0.998 / Rpim(I) all: 0.071 / Net I/σ(I): 9.4
Reflection shellResolution: 1.91→1.98 Å / Redundancy: 19.15 % / Num. unique obs: 13158 / CC1/2: 0.205 / % possible all: 99.06

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→46.55 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.31 / Phase error: 23.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2092 1993 1.04 %Random selection
Rwork0.178 ---
obs0.1783 101450 99.95 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→46.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10946 0 20 743 11709
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00911268
X-RAY DIFFRACTIONf_angle_d1.07515284
X-RAY DIFFRACTIONf_dihedral_angle_d8.5231540
X-RAY DIFFRACTIONf_chiral_restr0.071695
X-RAY DIFFRACTIONf_plane_restr0.0091983
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.150.31891440.320913606X-RAY DIFFRACTION100
2.15-2.210.34081400.298613501X-RAY DIFFRACTION100
2.21-2.280.28751450.275413565X-RAY DIFFRACTION100
2.28-2.350.28651410.258613588X-RAY DIFFRACTION100
2.35-2.430.29971390.24213539X-RAY DIFFRACTION100
2.43-2.530.28681430.23413614X-RAY DIFFRACTION100
2.53-2.650.22521400.21413560X-RAY DIFFRACTION100
2.65-2.790.21651420.200913575X-RAY DIFFRACTION100
2.79-2.960.2291470.186913570X-RAY DIFFRACTION100
2.96-3.190.21351400.180313545X-RAY DIFFRACTION100
3.19-3.510.19351380.16113579X-RAY DIFFRACTION100
3.51-4.020.15481470.14113539X-RAY DIFFRACTION100
4.02-5.060.16171440.127813600X-RAY DIFFRACTION100
5.06-46.550.19011430.150713539X-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)
10.5050.0628-0.20660.7288-0.18010.8408-0.0354-0.06980.00670.0803-0.04-0.1970.01740.35170.03960.29080.02990.01290.42850.08910.3655-34.2202-49.0482-24.0468
20.81610.3044-0.20491.40190.53842.10490.04670.07550.2477-0.0157-0.09250.3101-0.3009-0.26780.07520.26470.04470.0210.31390.07380.3736-57.955-34.8461-27.6266
32.394-0.00340.20981.5352-1.45052.04520.0586-0.53520.22570.4837-0.0966-0.021-0.46640.12570.03470.5318-0.04220.03140.4615-0.03160.3973-41.8569-27.0977-1.2226
42.9002-0.3334-0.38021.31860.64521.0634-0.0133-0.2111-0.19650.2152-0.0518-0.0444-0.05460.4570.07190.4912-0.0223-0.00210.53220.05130.3748-37.7502-36.9297-4.9178
50.66290.0002-0.46920.788-0.03752.00770.0424-0.15690.0990.172-0.0527-0.0711-0.19340.31090.00650.2533-0.0177-0.00480.33570.05120.3347-37.1454-28.9722-26.2666
60.66630.09590.09511.1387-0.14831.4299-0.03930.09780.034-0.0920.035-0.06610.0120.2156-0.00130.246-0.0423-0.03340.2730.02580.240517.6899-58.0939-14.918
75.9651-2.19371.9941.3707-0.8931.7181-0.05540.38170.45670.0187-0.1273-0.2524-0.31750.16310.20710.404-0.1193-0.01520.41790.06870.341516.1449-39.5311-22.741
82.0157-0.5997-0.22142.1510.70752.8955-0.00960.28060.2428-0.18940.0311-0.0843-0.3054-0.1235-0.01380.3196-0.0405-0.03150.37370.12790.3338-0.8504-32.5874-43.3449
93.1361.5525-1.16592.2557-0.55312.3793-0.0420.16090.0289-0.11770.0451-0.0039-0.0083-0.03080.00310.28690.0014-0.01270.21080.00910.21890.9805-65.7862-45.3067
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 308 )
4X-RAY DIFFRACTION4chain 'A' and (resid 309 through 371 )
5X-RAY DIFFRACTION5chain 'A' and (resid 372 through 670 )
6X-RAY DIFFRACTION6chain 'B' and (resid 5 through 286 )
7X-RAY DIFFRACTION7chain 'B' and (resid 287 through 346 )
8X-RAY DIFFRACTION8chain 'B' and (resid 347 through 497 )
9X-RAY DIFFRACTION9chain 'B' and (resid 498 through 735 )

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