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- PDB-1pg3: Acetyl CoA Synthetase, Acetylated on Lys609 -

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Basic information

Entry
Database: PDB / ID: 1pg3
TitleAcetyl CoA Synthetase, Acetylated on Lys609
Componentsacetyl-CoA synthetase
KeywordsLIGASE / AMP-forming / Adenylate-forming / thioester-forming / Lysine acetylation
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, N-terminal domain / ANL, C-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, N-terminal domain / ANL, C-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. / AMP-dependent synthetase/ligase / AMP-binding enzyme / GMP Synthetase; Chain A, domain 3 / AMP-binding enzyme, C-terminal domain superfamily / 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 / FOURIER SYNTHESIS / Resolution: 2.3 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: 1NNN
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 1.3Apr 4, 2018Group: Advisory / Data collection / Category: diffrn_source / pdbx_unobs_or_zero_occ_atoms / Item: _diffrn_source.type
Revision 1.4Oct 27, 2021Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / 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 1.5Aug 16, 2023Group: 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

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)147,10014
Polymers144,3652
Non-polymers2,73512
Water6,792377
1
A: acetyl-CoA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,5507
Polymers72,1821
Non-polymers1,3676
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: acetyl-CoA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,5507
Polymers72,1821
Non-polymers1,3676
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.981, 143.160, 71.934
Angle α, β, γ (deg.)90.00, 91.57, 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 , 5 types, 389 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#4: 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
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 377 / 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: 2.12 Å3/Da / Density % sol: 41.6 %
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: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 6, 2002 / Details: Osmic Max-Flux confocal focusing mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.29→24.21 Å / Num. all: 53761 / Num. obs: 51511 / % possible obs: 95.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 24 Å2 / Rsym value: 0.101 / Net I/σ(I): 7.9
Reflection shellResolution: 2.29→2.38 Å / Mean I/σ(I) obs: 1.7 / Num. unique all: 4037 / Rsym value: 0.384 / % possible all: 78.3
Reflection
*PLUS
Highest resolution: 2.3 Å / Num. obs: 177381 / % possible obs: 95.9 % / Num. measured all: 51552 / Rmerge(I) obs: 0.105
Reflection shell
*PLUS
Highest resolution: 2.3 Å / % possible obs: 78.3 % / Num. unique obs: 4037 / Num. measured obs: 9516 / Rmerge(I) obs: 0.384

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1NNM

1nnm
PDB Unreleased entry


Resolution: 2.3→24.22 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.236 2608 -random, same as 1NNM r-free set
Rwork0.196 ---
all-53547 --
obs-51411 96 %-
Displacement parametersBiso mean: 23.06 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å2-2.24 Å2
2---1.42 Å20 Å2
3---1.37 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.31 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 2.3→24.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9835 0 174 377 10386
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_d1.18
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 (%)
2.3-2.40.2862710.2460.017540780.7
2.4-2.530.2873170.230.016636895.3
2.53-2.690.2822980.2130.016646396.1
2.69-2.90.2863190.2160.016651997.3
2.9-3.190.2483510.2020.013659998.1
3.19-3.650.2263610.1980.012667299.2
3.65-4.590.1983470.1630.011670999.7
4.59-24.220.2153530.1930.011677499.7
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 30 Å / Rfactor Rfree: 0.239 / Rfactor Rwork: 0.199
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.2
LS refinement shell
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 2.44 Å / Rfactor Rfree: 0.283 / Rfactor Rwork: 0.25

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