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- PDB-7nyp: monomeric acetyl-CoA synthase in closed conformation -

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Basic information

Entry
Database: PDB / ID: 7nyp
Titlemonomeric acetyl-CoA synthase in closed conformation
ComponentsCO-methylating acetyl-CoA synthase
KeywordsOXIDOREDUCTASE / metalloprotein / nickel / 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
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: 2.1 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)167,35612
Polymers164,9692
Non-polymers2,38710
Water17,547974
1
A: CO-methylating acetyl-CoA synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,0605
Polymers82,4851
Non-polymers5754
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: CO-methylating acetyl-CoA synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,2967
Polymers82,4851
Non-polymers1,8126
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.950, 99.478, 238.289
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
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and resid 4 through 735)
d_2ens_1(chain "B" and resid 4 through 735)

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1VALLEUA1 - 729
d_12ens_1NINIB
d_13ens_1NINIC
d_14ens_1SF4SF4D
d_21ens_1VALLEUH1 - 729
d_22ens_1NINII
d_23ens_1NINIJ
d_24ens_1SF4SF4K

NCS oper: (Code: givenMatrix: (-0.903122381968, -0.421361284367, -0.0826113262561), (-0.418394305583, 0.90681678123, -0.0512789463184), (0.0965202996504, -0.0117470556616, -0.995261693445)Vector: -34. ...NCS oper: (Code: given
Matrix: (-0.903122381968, -0.421361284367, -0.0826113262561), (-0.418394305583, 0.90681678123, -0.0512789463184), (0.0965202996504, -0.0117470556616, -0.995261693445)
Vector: -34.9036546951, -6.04442440844, 95.6763444073)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein CO-methylating acetyl-CoA synthase


Mass: 82484.570 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 twinstrep-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 , 5 types, 984 molecules

#2: Chemical
ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ni / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: 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.: 2 / Source method: obtained synthetically / Formula: C18H18O21Ti
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 974 / 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: 2.51 Å3/Da / Density % sol: 51.05 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Lithium nitrate, 16% 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: May 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 2.1→46.44 Å / Num. obs: 96729 / % possible obs: 98.8 % / Redundancy: 2 % / Biso Wilson estimate: 32.07 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.039 / Rpim(I) all: 0.039 / Rrim(I) all: 0.056 / Net I/σ(I): 8.6
Reflection shellResolution: 2.1→2.18 Å / Rmerge(I) obs: 0.601 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 9478 / CC1/2: 0.585 / Rpim(I) all: 0.601 / Rrim(I) all: 0.849 / % possible all: 97.7

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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: 2.1→46.43 Å / SU ML: 0.254 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.0482
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2435 1887 2.35 %
Rwork0.1985 78344 -
obs0.1996 80231 81.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.11 Å2
Refinement stepCycle: LAST / Resolution: 2.1→46.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11532 0 114 974 12620
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008311920
X-RAY DIFFRACTIONf_angle_d1.243516178
X-RAY DIFFRACTIONf_chiral_restr0.05811748
X-RAY DIFFRACTIONf_plane_restr0.00892096
X-RAY DIFFRACTIONf_dihedral_angle_d22.98084500
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.887065110097 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.160.3923490.25492079X-RAY DIFFRACTION28.67
2.16-2.220.3045690.26552844X-RAY DIFFRACTION39.26
2.22-2.290.2788940.26723918X-RAY DIFFRACTION53.81
2.29-2.370.30121220.26325047X-RAY DIFFRACTION69.58
2.37-2.470.33271470.25476087X-RAY DIFFRACTION83.67
2.47-2.580.29311680.24376996X-RAY DIFFRACTION95.43
2.58-2.720.28241750.23397269X-RAY DIFFRACTION99.77
2.72-2.890.25681750.22727259X-RAY DIFFRACTION99.17
2.89-3.110.29311770.22927329X-RAY DIFFRACTION99.59
3.11-3.420.26461750.20737249X-RAY DIFFRACTION98.79
3.42-3.920.23731770.1777377X-RAY DIFFRACTION99.26
3.92-4.940.17791750.15247263X-RAY DIFFRACTION97.45
4.94-46.430.20411840.17177627X-RAY DIFFRACTION98.25

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