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- PDB-2xat: COMPLEX OF THE HEXAPEPTIDE XENOBIOTIC ACETYLTRANSFERASE WITH CHLO... -

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Basic information

Entry
Database: PDB / ID: 2xat
TitleCOMPLEX OF THE HEXAPEPTIDE XENOBIOTIC ACETYLTRANSFERASE WITH CHLORAMPHENICOL AND DESULFO-COENZYME A
ComponentsXENOBIOTIC ACETYLTRANSFERASE
KeywordsACETYLTRANSFERASE / XENOBIOTIC / CHLORAMPHENICOL / LEFT-HANDED BETA HELIX
Function / homology
Function and homology information


chloramphenicol O-acetyltransferase activity / chloramphenicol O-acetyltransferase / response to antibiotic
Similarity search - Function
: / Hexapeptide repeat / Hexapeptide repeat proteins / UDP N-Acetylglucosamine Acyltransferase; domain 1 / Bacterial transferase hexapeptide (six repeats) / Trimeric LpxA-like superfamily / 3 Solenoid / Mainly Beta
Similarity search - Domain/homology
CHLORAMPHENICOL / DESULFO-COENZYME A / Chloramphenicol acetyltransferase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsBeaman, T.W. / Sugantino, M. / Roderick, S.L.
Citation
Journal: Biochemistry / Year: 1998
Title: Structure of the hexapeptide xenobiotic acetyltransferase from Pseudomonas aeruginosa.
Authors: Beaman, T.W. / Sugantino, M. / Roderick, S.L.
#1: Journal: Proteins / Year: 1997
Title: Purification and Crystallization of Pseudomonas Aeruginosa Chloramphenicol Acetyltransferase
Authors: Tian, Y. / Beaman, T.W. / Roderick, S.L.
History
DepositionMar 11, 1998Processing site: BNL
Revision 1.0Jun 17, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: XENOBIOTIC ACETYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5653
Polymers23,5061
Non-polymers1,0592
Water00
1
A: XENOBIOTIC ACETYLTRANSFERASE
hetero molecules

A: XENOBIOTIC ACETYLTRANSFERASE
hetero molecules

A: XENOBIOTIC ACETYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,6959
Polymers70,5193
Non-polymers3,1766
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area14460 Å2
ΔGint-78 kcal/mol
Surface area22170 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)154.800, 154.800, 154.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number213
Space group name H-MP4132

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Components

#1: Protein XENOBIOTIC ACETYLTRANSFERASE


Mass: 23506.443 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PA103 / Cell line: BL21 / Plasmid: PYT1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P26841
#2: Chemical ChemComp-CLM / CHLORAMPHENICOL


Mass: 323.129 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H12Cl2N2O5 / Comment: antibiotic*YM
#3: Chemical ChemComp-DCA / DESULFO-COENZYME A


Mass: 735.469 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3

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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: 6.6 Å3/Da / Density % sol: 79 %
Crystal growpH: 8.5
Details: 10-20% POLYETHYLENEGLYCOL MONOMETHYL ETHER 2000, 100 MM TRIS, PH 8.5, 10 MM NICL2, 2 MM CHLORAMPHENICOL, 50 MM DESULFO-COA
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110-20 %mPEG20001reservoir
2100 mMTris-HCl1reservoir
310 mM1reservoirNiCl2

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Aug 1, 1997
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.2→99 Å / Num. obs: 10328 / % possible obs: 94 % / Redundancy: 3.8 % / Biso Wilson estimate: 22.7 Å2 / Rmerge(I) obs: 0.094 / Rsym value: 0.094 / Net I/σ(I): 10.9
Reflection shellResolution: 3.2→3.3 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.225 / Mean I/σ(I) obs: 4.9 / Rsym value: 0.225 / % possible all: 82
Reflection
*PLUS
Num. measured all: 42067
Reflection shell
*PLUS
% possible obs: 82 %

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Processing

Software
NameVersionClassification
PHASESphasing
X-PLOR3.851model building
X-PLOR3.851refinement
XENGENdata reduction
XENGENdata scaling
X-PLOR3.851phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→8 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.255 509 5.3 %RANDOM
Rwork0.213 ---
obs0.213 9553 93.8 %-
Displacement parametersBiso mean: 18 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.32 Å
Luzzati d res low-8 Å
Luzzati sigma a-0.2 Å
Refinement stepCycle: LAST / Resolution: 3.2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1564 0 67 0 1631
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.9
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.7
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 3.2→3.39 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.253 69 4.7 %
Rwork0.252 1401 -
obs--87.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2CLM.PARCLM.TOP
X-RAY DIFFRACTION3COADESULPHO_CAT.PARCOADESULPHO_CAT.TOP
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.9
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.7
LS refinement shell
*PLUS
Rfactor obs: 0.252

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