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- PDB-1ghe: CRYSTAL STRUCTURE OF TABTOXIN RESISTANCE PROTEIN COMPLEXED WITH A... -

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Basic information

Entry
Database: PDB / ID: 1ghe
TitleCRYSTAL STRUCTURE OF TABTOXIN RESISTANCE PROTEIN COMPLEXED WITH AN ACYL COENZYME A
ComponentsACETYLTRANSFERASE
KeywordsTRANSFERASE / Acyl Coenzyme A complex
Function / homology
Function and homology information


acyltransferase activity, transferring groups other than amino-acyl groups / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
Similarity search - Function
Acetyltransferase (GNAT) domain / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETYL COENZYME *A / Acetyltransferase
Similarity search - Component
Biological speciesPseudomonas syringae pv. tabaci (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.55 Å
AuthorsHe, H. / Ding, Y. / Bartlam, M. / Sun, F. / Le, Y. / Qin, X. / Tang, H. / Zhang, R. / Joachimiak, A. / Liu, Y. ...He, H. / Ding, Y. / Bartlam, M. / Sun, F. / Le, Y. / Qin, X. / Tang, H. / Zhang, R. / Joachimiak, A. / Liu, Y. / Zhao, N. / Rao, Z.
CitationJournal: J.Mol.Biol. / Year: 2003
Title: Crystal Structure of Tabtoxin Resistance Protein Complexed with Acetyl Coenzyme A Reveals the Mechanism for beta-Lactam Acetylation
Authors: He, H. / Ding, Y. / Bartlam, M. / Sun, F. / Le, Y. / Qin, X. / Tang, H. / Zhang, R. / Joachimiak, A. / Liu, Y. / Zhao, N. / Rao, Z.
History
DepositionDec 13, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 14, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _struct_conn.pdbx_leaving_atom_flag / _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

Downloads & links

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Assembly

Deposited unit
A: ACETYLTRANSFERASE
B: ACETYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,6044
Polymers38,9852
Non-polymers1,6192
Water2,918162
1
A: ACETYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,3022
Polymers19,4921
Non-polymers8101
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ACETYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,3022
Polymers19,4921
Non-polymers8101
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)101.76, 45.70, 84.24
Angle α, β, γ (deg.)90.00, 105.79, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein ACETYLTRANSFERASE / / TABTOXIN RESISTANCE PROTEIN


Mass: 19492.443 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas syringae pv. tabaci (bacteria)
Species: Pseudomonas amygdali / Plasmid: PQE-30 / Production host: Escherichia coli (E. coli)
References: UniProt: P16966, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Chemical ChemComp-ACO / ACETYL COENZYME *A / Acetyl-CoA


Mass: 809.571 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H38N7O17P3S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 162 / 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: 49.1 %
Crystal growTemperature: 291 K / Method: hanging drop/vapor diffusion / pH: 8
Details: PEG 4000, sodium acetate, Tris-HCL, pH 8.0, HANGING DROP/VAPOR DIFFUSION, temperature 291.0K
Crystal grow
*PLUS
Temperature: 291 K / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
125 mMTris-HCl1droppH8.0
2150 mM1dropNaCl
35 mMdithiothreitol1drop
41 mMPMSF1drop
50.2 mMsodium-EDTA1drop
620-25 mg/mlprotein1drop
7100 mMTris-HCl1reservoirpH8.0
836 %(w/v)PEG40001reservoir
90.21 M1reservoirNaAc

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Data collection

DiffractionMean temperature: 115 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9639
DetectorType: SBC-2 / Detector: CCD / Date: Sep 1, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9639 Å / Relative weight: 1
ReflectionResolution: 1.4→100 Å / Num. all: 105976 / Num. obs: 93060 / % possible obs: 95.3 % / Observed criterion σ(I): -3 / Redundancy: 3 % / Biso Wilson estimate: 13.4 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 5.9
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 1 % / Rmerge(I) obs: 0.32 / Num. unique all: 4747 / % possible all: 65
Reflection
*PLUS
Highest resolution: 1.49 Å / Lowest resolution: 100 Å / Num. obs: 56060 / % possible obs: 92 % / Num. measured all: 307917 / Rmerge(I) obs: 0.071
Reflection shell
*PLUS
Mean I/σ(I) obs: 2.5

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Processing

Software
NameVersionClassification
DENZO2000data reduction
SCALEPACK2000data scaling
O7model building
CNS1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementResolution: 1.55→30 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: CNS
RfactorNum. reflection% reflection
Rfree0.23 9026 -
Rwork0.209 --
all-73804 -
obs-70416 87.8 %
Refinement stepCycle: LAST / Resolution: 1.55→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2606 0 102 162 2870
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.02
X-RAY DIFFRACTIONc_angle_deg2.44
Refinement
*PLUS
Lowest resolution: 30 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.23
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.198
X-RAY DIFFRACTIONc_angle_deg2.4

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