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- PDB-2p20: Acetyl-CoA Synthetase, R584A mutation -

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Basic information

Entry
Database: PDB / ID: 2p20
TitleAcetyl-CoA Synthetase, R584A mutation
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, 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
ADENOSINE-5'-MONOPHOSPHATE-PROPYL ESTER / Acetyl-coenzyme A synthetase
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.22 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 6, 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 20, 2021Group: Database references / Derived calculations / Category: database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
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)145,0794
Polymers144,3012
Non-polymers7792
Water10,809600
1
A: Acetyl-coenzyme A synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,5402
Polymers72,1501
Non-polymers3891
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Acetyl-coenzyme A synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,5402
Polymers72,1501
Non-polymers3891
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.837, 95.408, 164.708
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: 72150.359 Da / Num. of mol.: 2 / Mutation: R584A
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-PRX / ADENOSINE-5'-MONOPHOSPHATE-PROPYL ESTER / ADENOSINE-5'-PROPYLPHOSPHATE


Mass: 389.301 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H20N5O7P / Details: according to Biochemistry, 41, 2379.
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 600 / 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: 2.5 Å3/Da / Density % sol: 50.78 %
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 Propyl-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: CHESS / Beamline: F2 / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 31, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.22→66.227 Å / Num. obs: 67992 / % possible obs: 92 % / Redundancy: 4.6 % / Biso Wilson estimate: 26.3 Å2 / Rmerge(I) obs: 0.062 / Rsym value: 0.062 / Net I/σ(I): 8.4
Reflection shellResolution: 2.22→2.32 Å / Redundancy: 3 % / Rmerge(I) obs: 0.314 / Mean I/σ(I) obs: 0.9 / Num. measured all: 19336 / Num. unique all: 6481 / Rsym value: 0.314 / % possible all: 61.6

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
REFMACrefinement
PDB_EXTRACT2data extraction
CHESSF2data collection
MOSFLMdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1PG4

1pg4


Resolution: 2.22→30 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.905 / SU B: 11.1 / SU ML: 0.147 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.287 / ESU R Free: 0.217 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23 3366 5 %RANDOM
Rwork0.176 ---
obs0.179 66709 93.01 %-
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: 18.929 Å2
Baniso -1Baniso -2Baniso -3
1--0.4 Å20 Å20 Å2
2---0.08 Å20 Å2
3---0.49 Å2
Refinement stepCycle: LAST / Resolution: 2.22→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9887 0 52 600 10539
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02210224
X-RAY DIFFRACTIONr_angle_refined_deg1.2451.94813954
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.02951276
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.25524.08451
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.244151583
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2231556
X-RAY DIFFRACTIONr_chiral_restr0.0820.21525
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.027866
X-RAY DIFFRACTIONr_nbd_refined0.1940.24735
X-RAY DIFFRACTIONr_nbtor_refined0.3020.26908
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.2698
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1660.232
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1750.219
X-RAY DIFFRACTIONr_mcbond_it0.5041.56509
X-RAY DIFFRACTIONr_mcangle_it0.835210230
X-RAY DIFFRACTIONr_scbond_it1.43434347
X-RAY DIFFRACTIONr_scangle_it2.2914.53723
LS refinement shellResolution: 2.22→2.272 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.367 134 -
Rwork0.28 2490 -
obs-2624 59.5 %
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)
10.64030.0301-0.02030.53270.03380.48170.0202-0.0391-0.0085-0.04780.004-0.0610.06920.0708-0.0242-0.06760.01610.0126-0.0366-0.0135-0.04452.581630.29316.8445
22.58270.1308-0.25922.26430.46612.77460.0309-0.2191-0.07850.2665-0.00290.1590.1282-0.1684-0.0281-0.0714-0.02040.0304-0.00590.0162-0.0371-17.778739.046840.3983
30.5674-0.1305-0.17730.40890.0760.87240.0489-0.02950.0941-0.09060.0476-0.0187-0.23480.0368-0.09650.0197-0.03870.0394-0.094-0.0153-0.0505-29.979575.234317.0896
41.24670.2784-0.05381.83520.16720.55970.0474-0.0293-0.07280.0426-0.04420.10010.0243-0.0231-0.0031-0.0812-0.0071-0.0019-0.0224-0.0022-0.0208-39.359544.611415.8823
Refinement TLS group

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

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA5 - 5175 - 517
22AA518 - 647518 - 647
33BB6 - 5176 - 517
44BB518 - 647518 - 647

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