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- PDB-3s2x: Structure of acetyl-Coenzyme A synthase Alpha subunit C-terminal ... -

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Basic information

Entry
Database: PDB / ID: 3s2x
TitleStructure of acetyl-Coenzyme A synthase Alpha subunit C-terminal domain
Componentsacetyl-CoA synthase subunit alpha
KeywordsTRANSFERASE
Function / homology
Function and homology information


CO-methylating acetyl-CoA synthase / CO-methylating acetyl-CoA synthase activity / : / acetyl-CoA metabolic process / carbon fixation / 4 iron, 4 sulfur cluster binding / metal ion binding
Similarity search - Function
Bifunctional carbon monoxide dehydrogenase/acetyl-coa synthase(codh/acs), Chain M, domain 5 / Bifunctional carbon monoxide dehydrogenase/acetyl-coa synthase(codh/acs), Chain M, domain 5 / 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 ...Bifunctional carbon monoxide dehydrogenase/acetyl-coa synthase(codh/acs), Chain M, domain 5 / Bifunctional carbon monoxide dehydrogenase/acetyl-coa synthase(codh/acs), Chain M, domain 5 / 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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICKEL (II) ION / Carbon monoxide dehydrogenase/acetyl-CoA synthase subunit alpha
Similarity search - Component
Biological speciesMoorella thermoacetica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.35 Å
AuthorsLi, P.
CitationJournal: Chembiochem / Year: 2011
Title: Insights into the Mechanistic Role of the [Fe(4) S(4) ] Cubane in the A-Cluster {[Fe(4) S(4) ]-(SR)-[Ni(p) Ni(d) ]} of Acetyl-Coenzyme A Synthase.
Authors: Liu, Y. / Wang, F. / Li, P. / Tan, X.
History
DepositionMay 17, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 27, 2011Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: acetyl-CoA synthase subunit alpha
B: acetyl-CoA synthase subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8476
Polymers29,6122
Non-polymers2354
Water25214
1
A: acetyl-CoA synthase subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9233
Polymers14,8061
Non-polymers1172
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: acetyl-CoA synthase subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9233
Polymers14,8061
Non-polymers1172
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)129.040, 129.040, 46.030
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein acetyl-CoA synthase subunit alpha / ACS subunit / CODH/ACS


Mass: 14806.085 Da / Num. of mol.: 2 / Fragment: C-terminal domain (UNP residues 594-729)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Moorella thermoacetica (bacteria) / Production host: Escherichia coli (E. coli)
References: UniProt: P27988, CO-methylating acetyl-CoA synthase
#2: Chemical
ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ni
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H2O

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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: 2.49 Å3/Da / Density % sol: 50.61 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 5.5 / Details: 15% ethanol, pH 5.5, EVAPORATION, temperature 298K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.49
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 20, 2006
RadiationMonochromator: Si Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.49 Å / Relative weight: 1
ReflectionResolution: 2.35→42.6 Å / Num. all: 11914 / Num. obs: 11621 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.4 % / Rmerge(I) obs: 0.078 / Rsym value: 0.078 / Net I/σ(I): 55.3
Reflection shellResolution: 2.35→2.43 Å / Redundancy: 8.6 % / Rmerge(I) obs: 0.456 / Mean I/σ(I) obs: 5 / Num. unique all: 1000 / Rsym value: 0.456 / % possible all: 83.2

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHENIXmodel building
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.35→42.6 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: THE ASSOCIATED STRUCTURE FACTOR FILE CONTAINS NO FREE R TEST SET FLAGS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2636 900 7.6 %RANDOM
Rwork0.221 10264 --
all-11914 --
obs-11164 93.7 %-
Solvent computationBsol: 48.1119 Å2
Displacement parametersBiso max: 92.46 Å2 / Biso mean: 59.5968 Å2 / Biso min: 35.42 Å2
Baniso -1Baniso -2Baniso -3
1-13.782 Å21.405 Å20 Å2
2--13.782 Å20 Å2
3----27.565 Å2
Refinement stepCycle: LAST / Resolution: 2.35→42.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2005 0 4 14 2023
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.36
X-RAY DIFFRACTIONc_bond_d0.008
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna.param
X-RAY DIFFRACTION3CNS_TOPPAR:ion.param
X-RAY DIFFRACTION4CNS_TOPPAR:water.param

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