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- PDB-7o0d: monomeric acetyl-CoA synthase in open conformation with methaneth... -

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Basic information

Entry
Database: PDB / ID: 7o0d
Titlemonomeric acetyl-CoA synthase in open conformation with methanethiol moiety of CoA bound to nickel proximal
ComponentsCO-methylating acetyl-CoA synthase
KeywordsOXIDOREDUCTASE / metalloprotein / nickel / acetogenesis / cluster A / ACS / CoA
Function / homology
Function and homology information


CO-methylating acetyl-CoA synthase / CO-methylating acetyl-CoA synthase activity / anaerobic carbon-monoxide dehydrogenase activity / acetyl-CoA metabolic process / 4 iron, 4 sulfur cluster binding / metal ion binding
Similarity search - Function
Bifunctional carbon monoxide dehydrogenase/acetyl-coa synthase(codh/acs), Chain M, domain 3 / Bifunctional carbon monoxide dehydrogenase/acetyl-coa synthase(codh/acs), Chain M, domain 3 / 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 / Prismane-like, alpha/beta-sandwich ...Bifunctional carbon monoxide dehydrogenase/acetyl-coa synthase(codh/acs), Chain M, domain 3 / Bifunctional carbon monoxide dehydrogenase/acetyl-coa synthase(codh/acs), Chain M, domain 3 / 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 / Prismane-like, alpha/beta-sandwich / Prismane-like superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
METHANETHIOL / NICKEL (II) ION / DI(HYDROXYETHYL)ETHER / Chem-PG6 / IRON/SULFUR CLUSTER / CO-methylating acetyl-CoA synthase
Similarity search - Component
Biological speciesCarboxydothermus hydrogenoformans Z-2901 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsKreibich, J. / Jeoung, J.H. / Dobbek, H.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research Foundation (DFG)DO785/5-2 Germany
German Research Foundation (DFG)EXC 2008 - 390540038 - UniSysCat Germany
CitationJournal: To Be Published
Title: Ligand binding at the Ni,Ni-[4Fe-4S] cluster of acetyl-CoA synthase
Authors: Kreibich, J. / Jeoung, J.H. / Dobbek, H.
History
DepositionMar 26, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 13, 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: CO-methylating acetyl-CoA synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,04224
Polymers82,4851
Non-polymers3,55723
Water5,242291
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5740 Å2
ΔGint-72 kcal/mol
Surface area32190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)199.344, 199.344, 168.268
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Space group name HallR32"
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x-y,-y,-z
#5: -x,-x+y,-z
#6: y,x,-z
#7: x+1/3,y+2/3,z+2/3
#8: -y+1/3,x-y+2/3,z+2/3
#9: -x+y+1/3,-x+2/3,z+2/3
#10: x-y+1/3,-y+2/3,-z+2/3
#11: -x+1/3,-x+y+2/3,-z+2/3
#12: y+1/3,x+2/3,-z+2/3
#13: x+2/3,y+1/3,z+1/3
#14: -y+2/3,x-y+1/3,z+1/3
#15: -x+y+2/3,-x+1/3,z+1/3
#16: x-y+2/3,-y+1/3,-z+1/3
#17: -x+2/3,-x+y+1/3,-z+1/3
#18: y+2/3,x+1/3,-z+1/3

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Components

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Protein , 1 types, 1 molecules A

#1: Protein CO-methylating acetyl-CoA synthase


Mass: 82484.570 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Carboxydothermus hydrogenoformans Z-2901 (bacteria)
Gene: acsB, CHY_1222 / Plasmid: pQE30
Details (production host): modified vector with twin-strep-tag and TEV cleavage site
Production host: Escherichia coli M15 (bacteria)
References: UniProt: Q3ACS4, CO-methylating acetyl-CoA synthase

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Non-polymers , 9 types, 314 molecules

#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4
#3: 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
#4: Chemical ChemComp-MEE / METHANETHIOL


Mass: 48.107 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH4S / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-PG6 / 1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE


Mass: 266.331 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H26O6
#6: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#7: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#8: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#9: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 291 / 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: 3.9 Å3/Da / Density % sol: 68.46 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop
Details: 150 mM MES pH 6.0, 2 M ammonium sulfate, 5% v/v PEG 300, 5 mM CoA trilithium salt

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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 PILATUS 6M-F / Detector: PIXEL / Date: Jul 16, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.3→48.88 Å / Num. obs: 56520 / % possible obs: 99.5 % / Redundancy: 2 % / Biso Wilson estimate: 44.44 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.027 / Rpim(I) all: 0.027 / Rrim(I) all: 0.038 / Net I/σ(I): 22.4
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 2 % / Rmerge(I) obs: 0.589 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 3807 / CC1/2: 0.613 / Rpim(I) all: 0.589 / Rrim(I) all: 0.833 / % possible all: 95.3

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Processing

Software
NameVersionClassification
XDSdata reduction
PHENIX1.18.2_3874refinement
XSCALEdata scaling
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RU3

1ru3


Resolution: 2.3→48.88 Å / SU ML: 0.2403 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.3302
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2218 1960 3.79 %
Rwork0.1964 49774 -
obs0.1974 51734 91.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 78.81 Å2
Refinement stepCycle: LAST / Resolution: 2.3→48.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5767 0 204 291 6262
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00396090
X-RAY DIFFRACTIONf_angle_d0.79368204
X-RAY DIFFRACTIONf_chiral_restr0.0481875
X-RAY DIFFRACTIONf_plane_restr0.00561040
X-RAY DIFFRACTIONf_dihedral_angle_d20.32772302
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.360.3462710.27031823X-RAY DIFFRACTION47.47
2.36-2.420.29521030.252614X-RAY DIFFRACTION67.07
2.42-2.490.27461160.2492946X-RAY DIFFRACTION75.92
2.49-2.570.28391340.243387X-RAY DIFFRACTION87.18
2.57-2.660.28631480.22513750X-RAY DIFFRACTION96.8
2.66-2.770.25271530.22683882X-RAY DIFFRACTION100
2.77-2.90.24571510.22273872X-RAY DIFFRACTION99.88
2.9-3.050.21551540.22523887X-RAY DIFFRACTION100
3.05-3.240.27121530.22713887X-RAY DIFFRACTION100
3.24-3.490.24411540.20683926X-RAY DIFFRACTION100
3.49-3.840.19531540.18063902X-RAY DIFFRACTION99.93
3.84-4.40.16611550.16753927X-RAY DIFFRACTION100
4.4-5.540.21511550.16543937X-RAY DIFFRACTION99.71
5.54-48.880.20731590.1894034X-RAY DIFFRACTION99.74

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