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- PDB-2p2f: Acetyl-CoA Synthetase, wild-type with acetate, AMP, and CoA bound -

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Basic information

Entry
Database: PDB / ID: 2p2f
TitleAcetyl-CoA Synthetase, wild-type with acetate, AMP, and CoA bound
ComponentsAcetyl-coenzyme A synthetase
KeywordsLIGASE / Adenylate-forming enzymes / Domain Alternation / Acyl-CoA ligase
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
ACETATE ION / ADENOSINE MONOPHOSPHATE / COENZYME A / Acetyl-coenzyme A synthetase
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.58 Å
AuthorsReger, A.S. / Gulick, A.M.
CitationJournal: Biochemistry / Year: 2007
Title: Biochemical and Crystallographic Analysis of Substrate Binding and Conformational Changes in Acetyl-CoA Synthetase.
Authors: Reger, A.S. / Carney, J.M. / Gulick, A.M.
History
DepositionMar 7, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Mar 13, 2024Group: Source and taxonomy / Structure summary / Category: entity / pdbx_entity_src_syn / Item: _entity.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Acetyl-coenzyme A synthetase
B: Acetyl-coenzyme A synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,8218
Polymers144,4732
Non-polymers2,3486
Water2,864159
1
A: Acetyl-coenzyme A synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,4104
Polymers72,2361
Non-polymers1,1743
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Acetyl-coenzyme A synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,4104
Polymers72,2361
Non-polymers1,1743
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.906, 94.933, 161.814
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Acetyl-coenzyme A synthetase / Acetate-CoA ligase / Acyl-activating enzyme


Mass: 72236.477 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Strain: Typhi / 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
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2 / Details: USB, 21608
#3: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36N7O16P3S / Details: Sigma, A-1752
#4: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Details: Sigma, C-4780 / Comment: AMP*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 159 / 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: 2.42 Å3/Da / Density % sol: 49.07 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 6-15% PEG 8000, 9-13% ethylene glycol, 50 mM BTP, 1 mM CoA, 1 mM Acetate, 1 mM AMP, 1 mM TCEP, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 287K

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.95 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Mar 28, 2003
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 2.58→81.65 Å / Num. obs: 42079 / % possible obs: 98.9 % / Redundancy: 5.1 % / Biso Wilson estimate: 38.3 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 10.8
Reflection shellResolution: 2.58→2.7 Å / Rmerge(I) obs: 0.224 / Mean I/σ(I) obs: 1 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
PDB_EXTRACT2data extraction
HKL-2000data reduction
SCALEPACKdata scaling
REFMAC5.2.0005phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: pdb entry 1PG4

1pg4


Resolution: 2.58→81.65 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.887 / SU B: 20.041 / SU ML: 0.211 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.238 / ESU R Free: 0.32 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.247 2261 5.1 %RANDOM
Rwork0.183 ---
obs0.186 42079 98.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 18.048 Å2
Baniso -1Baniso -2Baniso -3
1-0.71 Å20 Å20 Å2
2---1.14 Å20 Å2
3---0.43 Å2
Refinement stepCycle: LAST / Resolution: 2.58→81.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9828 0 150 159 10137
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02210247
X-RAY DIFFRACTIONr_angle_refined_deg1.5321.95914000
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.41651265
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.14823.996448
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.837151558
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.211557
X-RAY DIFFRACTIONr_chiral_restr0.0960.21521
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.027857
X-RAY DIFFRACTIONr_nbd_refined0.2110.24633
X-RAY DIFFRACTIONr_nbtor_refined0.310.26918
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1420.2468
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1790.220
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1480.25
X-RAY DIFFRACTIONr_mcbond_it0.6111.56445
X-RAY DIFFRACTIONr_mcangle_it1.019210159
X-RAY DIFFRACTIONr_scbond_it1.67234421
X-RAY DIFFRACTIONr_scangle_it2.6814.53841
LS refinement shellResolution: 2.58→2.647 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 144 -
Rwork0.226 2892 -
obs-3036 93.42 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.50340.07070.06930.61090.00770.41110.0265-0.0045-0.0027-0.0152-0.0147-0.03170.06530.0418-0.0117-0.0350.02280.0001-0.03660.0015-0.04982.462730.304716.3629
22.38590.6621-0.94463.16570.80983.6109-0.0067-0.02030.00780.3555-0.0860.22560.1709-0.19770.0927-0.0681-0.02710.0423-0.07980.0054-0.0274-17.407839.269339.6581
30.5323-0.0123-0.0890.39790.06620.76420.0137-0.00930.0365-0.01480.0330.0105-0.1378-0.0196-0.0467-0.02940.0178-0.0205-0.0584-0.0005-0.037-30.230474.973516.9745
40.65640.313-0.34023.28760.90951.78350.0719-0.0097-0.07570.1449-0.19380.26310.0407-0.07120.1219-0.09510.0005-0.0173-0.0176-0.02910.0182-38.76244.529215.9048
51.3441-1.96648.27922.8769-12.112650.9975-0.13120.25811.1218-1.7881-0.7965-1.8053-0.285-2.83620.92770.00140.0010.0017-0.00160.0036-0.0014-7.933143.296320.4865
642.793913.278324.06274.40486.810915.0392.3765-0.70.7963-0.8985-0.4427-3.35710.9041-0.6087-1.9338-0.0039-0.00180.0039-0.0015-0.0044-0.0008-22.990558.97615.801
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA6 - 5176 - 517
22AA518 - 647518 - 647
33BB5 - 5175 - 517
44BB518 - 647518 - 647
55AE9901
66BF9911

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