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- PDB-1pg4: Acetyl CoA Synthetase, Salmonella enterica -

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Basic information

Entry
Database: PDB / ID: 1pg4
TitleAcetyl CoA Synthetase, Salmonella enterica
Componentsacetyl-CoA synthetase
KeywordsLIGASE / AMP-forming / Adenylate-forming / thioester-forming
Function / homology
Function and homology information


acetate-CoA ligase / acetate-CoA ligase activity / acetyl-CoA biosynthetic process from acetate / acetyl-CoA biosynthetic process / AMP binding / chemotaxis / ATP binding / metal ion binding / cytosol
Similarity search - Function
Acetate-CoA ligase / Acetyl-coenzyme A synthetase, N-terminal domain / Acetyl-coenzyme A synthetase N-terminus / ANL, C-terminal domain / ANL, N-terminal domain / ANL, N-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding, conserved site / Putative AMP-binding domain signature. ...Acetate-CoA ligase / Acetyl-coenzyme A synthetase, N-terminal domain / Acetyl-coenzyme A synthetase N-terminus / ANL, C-terminal domain / ANL, N-terminal domain / ANL, N-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding, conserved site / Putative AMP-binding domain signature. / GMP Synthetase; Chain A, domain 3 / AMP-dependent synthetase/ligase / AMP-binding enzyme, C-terminal domain superfamily / AMP-binding enzyme / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
COENZYME A / ADENOSINE-5'-MONOPHOSPHATE-PROPYL ESTER / Acetyl-coenzyme A synthetase
Similarity search - Component
Biological speciesSalmonella enterica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.75 Å
AuthorsGulick, A.M. / Starai, V.J. / Horswill, A.R. / Homick, K.M. / Escalante-Semerena, J.C.
CitationJournal: Biochemistry / Year: 2003
Title: The 1.75 A Crystal Structure of Acetyl-CoA Synthetase Bound to Adenosine-5'-propylphosphate and Coenzyme A
Authors: Gulick, A.M. / Starai, V.J. / Horswill, A.R. / Homick, K.M. / Escalante-Semerena, J.C.
History
DepositionMay 27, 2003Deposition site: RCSB / Processing site: RCSB
SupersessionJun 3, 2003ID: 1NNM
Revision 1.0Jun 3, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_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_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: acetyl-CoA synthetase
B: acetyl-CoA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,10815
Polymers144,3652
Non-polymers2,74413
Water15,295849
1
A: acetyl-CoA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,5858
Polymers72,1821
Non-polymers1,4037
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: acetyl-CoA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,5237
Polymers72,1821
Non-polymers1,3416
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.994, 143.016, 71.731
Angle α, β, γ (deg.)90.00, 91.32, 90.00
Int Tables number4
Cell settingmonoclinic
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein acetyl-CoA synthetase / / E.C.6.2.1.1


Mass: 72182.422 Da / Num. of mol.: 2 / Mutation: R174C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica (bacteria) / Gene: ACS / Plasmid: pTYB1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8ZKF6, acetate-CoA ligase

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Non-polymers , 6 types, 862 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-COA / COENZYME A / Coenzyme A


Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#5: Chemical ChemComp-PRX / ADENOSINE-5'-MONOPHOSPHATE-PROPYL ESTER / ADENOSINE-5'-PROPYLPHOSPHATE


Mass: 389.301 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H20N5O7P
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 849 / 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: 2.03 Å3/Da / Density % sol: 38.9 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 8000, ethylene glycol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 287K
Crystal grow
*PLUS
Temperature: 14 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
21 mMCoA1drop
31 mMTCEP1drop
41 mMadenosine-5'-propylphosphate1drop
510-14 %PEG80001reservoir
610 %ethylene glycol1reservoir
750 mMMES1reservoirpH6.5

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F2 / Wavelength: 0.98074 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 26, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98074 Å / Relative weight: 1
ReflectionResolution: 1.75→29.8 Å / Num. all: 121298 / Num. obs: 114107 / % possible obs: 93.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 19.4 Å2 / Rsym value: 0.071 / Net I/σ(I): 14.2
Reflection shellResolution: 1.75→1.81 Å / Mean I/σ(I) obs: 2 / Num. unique all: 2926 / Rsym value: 0.415 / % possible all: 75.1
Reflection
*PLUS
Num. obs: 114217 / Num. measured all: 402947 / Rmerge(I) obs: 0.071
Reflection shell
*PLUS
% possible obs: 75.1 % / Num. unique obs: 2926 / Num. measured obs: 5608 / Rmerge(I) obs: 0.415

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNS1refinement
RefinementMethod to determine structure: MIR / Resolution: 1.75→29.8 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.211 5695 5 %random
Rwork0.184 ---
all-121298 --
obs-113617 93.7 %-
Displacement parametersBiso mean: 21.22 Å2
Baniso -1Baniso -2Baniso -3
1--2.06 Å20 Å2-2.74 Å2
2---0.77 Å20 Å2
3---2.83 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 1.75→29.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9816 0 172 849 10837
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRfactor Rfree errorNum. reflection obs% reflection obs (%)
1.75-1.830.2856060.2880.0121179478
1.83-1.930.2396500.2410.0091329887.6
1.93-2.050.1966570.1960.0081363890.1
2.05-2.20.1877260.1940.0071494394.6
2.2-2.430.1817350.1790.0071494398.5
2.43-3.780.1787170.1780.0071513599.8
2.78-3.50.1778010.1770.00615175100
3.5-29.80.1688030.1680.00615297100
Refinement
*PLUS
Lowest resolution: 30 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Lowest resolution: 1.86 Å / Rfactor Rfree: 0.309 / Rfactor Rwork: 0.281

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