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- PDB-7nys: monomeric acetyl-CoA synthase in closed conformation with carbon ... -

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Basic information

Entry
Database: PDB / ID: 7nys
Titlemonomeric acetyl-CoA synthase in closed conformation with carbon monoxide bound to the Ni proximal of cluster A
ComponentsCO-methylating acetyl-CoA synthase
KeywordsOXIDOREDUCTASE / carbon monoxide / nickel / acetogenesis / cluster A / ACS / metalloprotein
Function / homology
Function and homology information


CO-methylating acetyl-CoA synthase / CO-methylating acetyl-CoA synthase activity / : / acetyl-CoA metabolic process / 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 / Prismane-like, alpha/beta-sandwich / Prismane-like superfamily
Similarity search - Domain/homology
MALONATE ION / NICKEL (II) ION / DI(HYDROXYETHYL)ETHER / IRON/SULFUR CLUSTER / Chem-UW8 / $l^{3}-oxidanylidynemethylnickel / CO-methylating acetyl-CoA synthase
Similarity search - Component
Biological speciesCarboxydothermus hydrogenoformans Z-2901 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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)167,36719
Polymers164,8552
Non-polymers2,51217
Water28,1931565
1
A: CO-methylating acetyl-CoA synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,9956
Polymers82,4281
Non-polymers5685
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: CO-methylating acetyl-CoA synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,37113
Polymers82,4281
Non-polymers1,94412
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.276, 99.200, 238.584
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 5 through 264 or resid 266...
d_2ens_1(chain "B" and (resid 5 through 264 or resid 266...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1ILEVALA1 - 260
d_12ens_1THRGLUA263 - 331
d_13ens_1ILEGLUA333 - 397
d_14ens_1PHEILEA400 - 532
d_15ens_1TRPHISA535 - 620
d_16ens_1GLYLEUA623 - 732
d_17ens_1SF4SF4B
d_18ens_15CZ5CZC
d_21ens_1ILEVALH2 - 261
d_22ens_1THRGLUH263 - 331
d_23ens_1ILEGLUH334 - 398
d_24ens_1PHEILEH401 - 533
d_25ens_1TRPHISH535 - 620
d_26ens_1GLYLEUH622 - 731
d_27ens_1SF4SF4I
d_28ens_15CZ5CZJ

NCS oper: (Code: givenMatrix: (-0.90630363928, -0.414257580658, -0.0836921160914), (-0.41211652927, 0.910151816827, -0.0422331224303), (0.0936679226363, -0.00378512814592, -0.995596300251)Vector: -34. ...NCS oper: (Code: given
Matrix: (-0.90630363928, -0.414257580658, -0.0836921160914), (-0.41211652927, 0.910151816827, -0.0422331224303), (0.0936679226363, -0.00378512814592, -0.995596300251)
Vector: -34.8591690211, -6.29572670707, 95.7379570712)

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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, 1582 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-UWE / $l^{3}-oxidanylidynemethylnickel


Mass: 86.703 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CNiO / 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
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: 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
#7: Chemical
ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H2O4
#8: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1565 / 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: 2.52 Å3/Da / Density % sol: 51.24 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop
Details: 0.1 M sodium malonate pH 6, 20% 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: Mar 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 2→48.56 Å / Num. obs: 112519 / % possible obs: 99.2 % / Redundancy: 2 % / Biso Wilson estimate: 25.25 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.048 / Rrim(I) all: 0.067 / Net I/σ(I): 9.1
Reflection shellResolution: 2→2.05 Å / Rmerge(I) obs: 0.629 / Mean I/σ(I) obs: 1 / Num. unique obs: 7917 / CC1/2: 0.574 / Rpim(I) all: 0.629 / Rrim(I) all: 0.889 / % possible all: 99.4

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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→48.56 Å / SU ML: 0.2273 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.2249
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2214 1927 2.01 %
Rwork0.1842 93993 -
obs0.185 95920 84.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.21 Å2
Refinement stepCycle: LAST / Resolution: 2→48.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11525 0 122 1565 13212
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008411960
X-RAY DIFFRACTIONf_angle_d0.97716213
X-RAY DIFFRACTIONf_chiral_restr0.05761749
X-RAY DIFFRACTIONf_plane_restr0.0072111
X-RAY DIFFRACTIONf_dihedral_angle_d21.46784507
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.854103675391 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.050.2873400.24721940X-RAY DIFFRACTION24.86
2.05-2.110.3727570.25222803X-RAY DIFFRACTION35.64
2.11-2.170.3213840.24184061X-RAY DIFFRACTION51.7
2.17-2.240.27891290.23746288X-RAY DIFFRACTION80.28
2.24-2.320.26191560.23177665X-RAY DIFFRACTION97.47
2.32-2.410.26071610.21247859X-RAY DIFFRACTION99.6
2.41-2.520.26771620.20027847X-RAY DIFFRACTION99.42
2.52-2.650.23171600.19757827X-RAY DIFFRACTION99.28
2.65-2.820.22471610.19437853X-RAY DIFFRACTION98.88
2.82-3.040.25831620.20117892X-RAY DIFFRACTION99.7
3.04-3.340.23231620.19147912X-RAY DIFFRACTION99.3
3.34-3.830.19911620.16527927X-RAY DIFFRACTION98.96
3.83-4.820.16811620.14067904X-RAY DIFFRACTION98.23
4.82-48.560.1891690.16888215X-RAY DIFFRACTION97.93

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