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- PDB-1pd5: Crystal structure of E.coli chloramphenicol acetyltransferase typ... -

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Basic information

Entry
Database: PDB / ID: 1pd5
TitleCrystal structure of E.coli chloramphenicol acetyltransferase type I at 2.5 Angstrom resolution
ComponentsChloramphenicol acetyltransferase
KeywordsTRANSFERASE / trimer / chloramphenicol / acetyltransferase
Function / homology
Function and homology information


chloramphenicol O-acetyltransferase activity / chloramphenicol O-acetyltransferase / response to antibiotic
Similarity search - Function
Chloramphenicol acetyltransferase, active site / Chloramphenicol acetyltransferase active site. / Chloramphenicol acetyltransferase / Chloramphenicol acetyltransferase / Chloramphenicol acetyltransferase / Chloramphenicol acetyltransferase-like domain / Chloramphenicol Acetyltransferase / Chloramphenicol acetyltransferase-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chloramphenicol acetyltransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsRoidis, A. / Kokkinidis, M.
Citation
Journal: To be Published
Title: Crystal structure of E.coli chloramphenicol acetyltransferase type I at 2.5 Angstrom resolution
Authors: Roidis, A. / Kokkinidis, M.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2000
Title: Crystallization of type I chloramphenicol acetyltransferase:an approach based on the concept of ionic strength reducers
Authors: Andreeva, A.E. / Borissova, B.E. / Mironova, R. / Glykos, N.M. / Kotsifaki, D. / Ivanov, I. / Krysteva, M. / Kokkinidis, M.
History
DepositionMay 19, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 1, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Aug 16, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Chloramphenicol acetyltransferase
B: Chloramphenicol acetyltransferase
C: Chloramphenicol acetyltransferase
D: Chloramphenicol acetyltransferase
E: Chloramphenicol acetyltransferase
F: Chloramphenicol acetyltransferase
G: Chloramphenicol acetyltransferase
H: Chloramphenicol acetyltransferase
I: Chloramphenicol acetyltransferase
J: Chloramphenicol acetyltransferase
K: Chloramphenicol acetyltransferase
L: Chloramphenicol acetyltransferase


Theoretical massNumber of molelcules
Total (without water)308,30612
Polymers308,30612
Non-polymers00
Water3,747208
1
A: Chloramphenicol acetyltransferase
B: Chloramphenicol acetyltransferase
C: Chloramphenicol acetyltransferase


Theoretical massNumber of molelcules
Total (without water)77,0763
Polymers77,0763
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6470 Å2
ΔGint-38 kcal/mol
Surface area27040 Å2
MethodPISA
2
D: Chloramphenicol acetyltransferase
E: Chloramphenicol acetyltransferase
F: Chloramphenicol acetyltransferase


Theoretical massNumber of molelcules
Total (without water)77,0763
Polymers77,0763
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6530 Å2
ΔGint-36 kcal/mol
Surface area27470 Å2
MethodPISA
3
G: Chloramphenicol acetyltransferase
H: Chloramphenicol acetyltransferase
I: Chloramphenicol acetyltransferase


Theoretical massNumber of molelcules
Total (without water)77,0763
Polymers77,0763
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6530 Å2
ΔGint-38 kcal/mol
Surface area26830 Å2
MethodPISA
4
J: Chloramphenicol acetyltransferase
K: Chloramphenicol acetyltransferase
L: Chloramphenicol acetyltransferase


Theoretical massNumber of molelcules
Total (without water)77,0763
Polymers77,0763
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6610 Å2
ΔGint-36 kcal/mol
Surface area27210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.739, 129.702, 117.984
Angle α, β, γ (deg.)90.00, 108.38, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is a trimer. There are four trimers in the asymmetric unit ABC,DEF,GHI,JKL

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Components

#1: Protein
Chloramphenicol acetyltransferase


Mass: 25692.145 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: CAT OR HCM1.206 / Plasmid: pBR322 / Production host: Escherichia coli (E. coli) / Strain (production host): LE392
References: UniProt: P62577, chloramphenicol O-acetyltransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 208 / 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: 2.73 Å3/Da / Density % sol: 54.86 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: methanol,calcium chloride,MES, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 290.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.81 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 28, 2002 / Details: Bent mirror
RadiationMonochromator: Triangular monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.81 Å / Relative weight: 1
ReflectionResolution: 2.5→10 Å / Num. all: 114277 / Num. obs: 114277 / % possible obs: 99.6 % / Observed criterion σ(F): 13.91 / Observed criterion σ(I): 12.6 / Redundancy: 3.28 % / Rmerge(I) obs: 0.065 / Rsym value: 0.061
Reflection shellResolution: 2.5→2.59 Å / Rmerge(I) obs: 0.291 / Num. unique all: 9674 / Rsym value: 0.246 / % possible all: 99.2

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MAR345data collection
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3CLA

3cla


Resolution: 2.5→10 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.892 / SU B: 9.945 / SU ML: 0.224 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.518 / ESU R Free: 0.324 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.28139 5537 5 %RANDOM
Rwork0.19478 ---
obs0.19912 105347 98.64 %-
all-114277 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 46.425 Å2
Baniso -1Baniso -2Baniso -3
1-5.92 Å20 Å21.74 Å2
2---2.96 Å20 Å2
3----1.86 Å2
Refinement stepCycle: LAST / Resolution: 2.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21210 0 0 208 21418
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0410.02121882
X-RAY DIFFRACTIONr_angle_refined_deg2.9471.89529698
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.98152546
X-RAY DIFFRACTIONr_chiral_restr0.2140.23052
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0217196
X-RAY DIFFRACTIONr_nbd_refined0.2690.210256
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1720.2921
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2630.296
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4180.213
X-RAY DIFFRACTIONr_mcbond_it1.5091.512751
X-RAY DIFFRACTIONr_mcangle_it2.705220627
X-RAY DIFFRACTIONr_scbond_it4.39739131
X-RAY DIFFRACTIONr_scangle_it6.2244.59071
LS refinement shellResolution: 2.5→2.561 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.355 349
Rwork0.271 6609

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