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- PDB-7nz5: monomeric acetyl-CoA synthase with Zn at the proximal position of... -

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Basic information

Entry
Database: PDB / ID: 7nz5
Titlemonomeric acetyl-CoA synthase with Zn at the proximal position of cluster A
ComponentsCO-methylating acetyl-CoA synthase
KeywordsOXIDOREDUCTASE / metalloprotein / nickel / zinc / acetogenesis / cluster A / ACS
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
(R,R)-2,3-BUTANEDIOL / CITRIC ACID / NICKEL (II) ION / DI(HYDROXYETHYL)ETHER / IRON/SULFUR CLUSTER / Chem-UW8 / CO-methylating acetyl-CoA synthase
Similarity search - Component
Biological speciesCarboxydothermus hydrogenoformans Z-2901 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 23, 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
B: CO-methylating acetyl-CoA synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)167,92421
Polymers164,8552
Non-polymers3,06919
Water27,7071538
1
A: CO-methylating acetyl-CoA synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,72315
Polymers82,4281
Non-polymers2,29514
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: CO-methylating acetyl-CoA synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,2026
Polymers82,4281
Non-polymers7745
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.246, 98.811, 238.875
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein CO-methylating acetyl-CoA synthase


Mass: 82427.516 Da / Num. of mol.: 2
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 , 8 types, 1557 molecules

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


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: 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
#5: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H8O7
#7: Chemical ChemComp-UW8 / 2-[3,8,8,12,12-pentakis(2-hydroxy-2-oxoethyl)-2,7,11-tris(oxidanylidene)-1,4,6,9,10,13-hexaoxa-5$l^{6}-titanaspiro[4.4^{5}.4^{5}]tridecan-3-yl]ethanoic acid


Mass: 618.190 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H18O21Ti
#8: Chemical ChemComp-BU3 / (R,R)-2,3-BUTANEDIOL


Mass: 90.121 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O2
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1538 / 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: 2.48 Å3/Da / Density % sol: 50.38 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop
Details: 70 mM Bis-Tris-Propane pH 7.6, 30 mM citric acid, 24% w/v PEG 3350, 5 mM Ti(III)citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jan 18, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 1.9→46.19 Å / Num. obs: 127825 / % possible obs: 98.5 % / Redundancy: 2 % / Biso Wilson estimate: 19.93 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.031 / Rpim(I) all: 0.031 / Rrim(I) all: 0.044 / Net I/σ(I): 9.4
Reflection shellResolution: 1.9→1.95 Å / Rmerge(I) obs: 0.451 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 9008 / CC1/2: 0.839 / Rpim(I) all: 0.451 / Rrim(I) all: 0.638

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Processing

Software
NameVersionClassification
XDS1.18.2_3874data reduction
PHENIX1.18.2_3874refinement
XSCALEdata scaling
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RU3

1ru3


Resolution: 1.9→46.19 Å / SU ML: 0.1805 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.0497
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2239 1897 1.66 %
Rwork0.1933 112374 -
obs0.1938 114271 88.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.01 Å2
Refinement stepCycle: LAST / Resolution: 1.9→46.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11532 0 157 1538 13227
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.010911976
X-RAY DIFFRACTIONf_angle_d1.224216229
X-RAY DIFFRACTIONf_chiral_restr0.0641752
X-RAY DIFFRACTIONf_plane_restr0.00872104
X-RAY DIFFRACTIONf_dihedral_angle_d22.16164514
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.950.3763550.25963298X-RAY DIFFRACTION36.6
1.95-20.3141850.25335006X-RAY DIFFRACTION55.62
2-2.060.26121060.23856272X-RAY DIFFRACTION69.39
2.06-2.130.26191310.23717757X-RAY DIFFRACTION86.15
2.13-2.20.25561470.22748705X-RAY DIFFRACTION96.29
2.2-2.290.26961510.21458942X-RAY DIFFRACTION98.85
2.29-2.390.24221500.20268927X-RAY DIFFRACTION98.55
2.39-2.520.23221480.19928782X-RAY DIFFRACTION96.78
2.52-2.680.21831530.20129036X-RAY DIFFRACTION99.14
2.68-2.880.21751530.20099044X-RAY DIFFRACTION99.29
2.88-3.170.24711520.20529054X-RAY DIFFRACTION99.05
3.17-3.630.19391530.18128994X-RAY DIFFRACTION98.13
3.63-4.580.20071540.15339170X-RAY DIFFRACTION99.11
4.58-46.190.19221590.17689387X-RAY DIFFRACTION97.65

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