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- PDB-8cjc: F515A variant of the CODH/ACS complex of C. hydrogenoformans -

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Basic information

Entry
Database: PDB / ID: 8cjc
TitleF515A 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 / : / acetyl-CoA metabolic process / hydroxylamine reductase activity / nickel cation binding / generation of precursor metabolites and energy / response to hydrogen peroxide ...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 / response to hydrogen peroxide / peroxidase activity / 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: 2.22 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 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.
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

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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)158,21415
Polymers156,1602
Non-polymers2,05313
Water16,916939
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

A: Carbon monoxide dehydrogenase
B: CO-methylating acetyl-CoA synthase
hetero molecules

A: Carbon monoxide dehydrogenase
B: CO-methylating acetyl-CoA synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)632,85460
Polymers624,6418
Non-polymers8,21352
Water1448
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 area22690 Å2
ΔGint-353 kcal/mol
Surface area88670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)142.130, 142.130, 290.720
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-1142-

HOH

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Carbon monoxide dehydrogenase


Mass: 74125.219 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: 82035.078 Da / Num. of mol.: 1 / Mutation: F515A
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, 952 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 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 3 / 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.: 939 / 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: 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 21.2 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 21.2 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: Dec 9, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.99→48.45 Å / Num. obs: 119052 / % possible obs: 99.91 % / Redundancy: 39.8 % / CC1/2: 0.998 / Rpim(I) all: 0.069 / Net I/σ(I): 12.3
Reflection shellResolution: 1.99→2.06 Å / Redundancy: 40.22 % / Mean I/σ(I) obs: 0.8 / Num. unique obs: 11631 / CC1/2: 0.397 / % possible all: 99.19

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.22→45 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2021 2099 2.43 %
Rwork0.1577 --
obs0.1588 86360 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.22→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10900 0 62 939 11901
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111269
X-RAY DIFFRACTIONf_angle_d1.01215290
X-RAY DIFFRACTIONf_dihedral_angle_d7.4981544
X-RAY DIFFRACTIONf_chiral_restr0.0611696
X-RAY DIFFRACTIONf_plane_restr0.0081984
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.22-2.270.28221360.22535455X-RAY DIFFRACTION99
2.27-2.320.22251390.19945546X-RAY DIFFRACTION100
2.32-2.390.22511370.18355517X-RAY DIFFRACTION100
2.39-2.460.21921380.17985549X-RAY DIFFRACTION100
2.46-2.540.23531390.18385547X-RAY DIFFRACTION100
2.54-2.630.24771380.18235546X-RAY DIFFRACTION100
2.63-2.730.22911380.17395560X-RAY DIFFRACTION100
2.73-2.860.2231390.16755554X-RAY DIFFRACTION100
2.86-3.010.20621390.16145602X-RAY DIFFRACTION100
3.01-3.20.21661390.16115588X-RAY DIFFRACTION100
3.2-3.440.21471410.15365633X-RAY DIFFRACTION100
3.44-3.790.17881400.13935636X-RAY DIFFRACTION100
3.79-4.340.1741420.12845698X-RAY DIFFRACTION100
4.34-5.460.16281440.13435778X-RAY DIFFRACTION100
5.46-450.19281500.16096052X-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)
10.28440.2747-0.28490.8509-0.16460.599-0.0312-0.0925-0.03760.0863-0.0503-0.18880.03560.24920.07360.18210.0240.0130.35520.07190.3188-28.0677-50.9741-24.5147
21.2129-0.5135-1.21411.5981.44483.07750.07450.07880.16310.0213-0.08170.1922-0.3145-0.3470.02350.1590.02010.02350.18850.05810.2483-58.1712-33.9557-25.4863
30.4382-0.1007-0.41240.5278-0.11970.66390.0112-0.0560.03650.1169-0.04980.0076-0.05050.05330.0280.19240.00860.00580.21980.05950.2196-46.9671-37.9271-21.1989
44.15980.5015-0.02562.55930.08452.54150.0244-0.34050.01790.267-0.0534-0.0456-0.12130.2830.02020.2764-0.0140.00660.25220.04140.1929-42.6656-35.8185-1.0535
50.6744-0.0279-0.21710.80070.28161.69650.0375-0.09770.1120.1089-0.0475-0.1027-0.20210.23880.01750.1584-0.03140.00850.2370.05060.226-35.1837-27.5047-30.7777
60.7053-0.02590.08531.2494-0.15461.4858-0.0210.12890.0371-0.13230.0086-0.0514-0.01680.13860.00490.1613-0.0359-0.01740.18470.02840.155717.8883-58.073-14.8424
78.5-3.38033.26981.624-1.53311.82960.03190.42450.41840.0124-0.1837-0.1973-0.22560.12680.18540.2991-0.09880.01530.29320.05550.22316.84-39.7859-22.3665
82.0097-0.5953-0.52731.76431.07773.68350.01170.1720.1345-0.11880.04470.0074-0.1187-0.1846-0.06930.214-0.0344-0.02740.23560.11060.2501-0.6648-32.7892-43.3606
93.25921.5565-1.58361.9446-0.93882.5595-0.02370.1180.0507-0.08660.03030.0085-0.0302-0.0198-0.01010.23540.0056-0.01490.1332-0.00790.17811.0284-65.8475-45.3618
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 92 )
2X-RAY DIFFRACTION2chain 'A' and (resid 93 through 207 )
3X-RAY DIFFRACTION3chain 'A' and (resid 208 through 283 )
4X-RAY DIFFRACTION4chain 'A' and (resid 284 through 410 )
5X-RAY DIFFRACTION5chain 'A' and (resid 411 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 734 )

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