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- PDB-9m5s: Crystal structure of type A chloramphenicol acetyltransferase fro... -

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Basic information

Entry
Database: PDB / ID: 9m5s
TitleCrystal structure of type A chloramphenicol acetyltransferase from Staphylococcus aureus at 1.8 angstrom resolution
ComponentsChloramphenicol acetyltransferase
KeywordsANTIBIOTIC
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 superfamily
Similarity search - Domain/homology
ACETATE ION / : / HEXANE-1,6-DIOL / Chloramphenicol acetyltransferase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsWang, K. / Chen, J. / Ye, S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structure of type I chloramphenicol acetyltransferase from Staphylococcus aureus
Authors: Wang, K. / Chen, J. / Ye, S.
History
DepositionMar 6, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Aug 27, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Chloramphenicol acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,33510
Polymers25,4491
Non-polymers8869
Water4,756264
1
A: Chloramphenicol acetyltransferase
hetero molecules

A: Chloramphenicol acetyltransferase
hetero molecules

A: Chloramphenicol acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,00430
Polymers76,3463
Non-polymers2,65827
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area10770 Å2
ΔGint-79 kcal/mol
Surface area27640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.551, 103.551, 46.249
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP321
Space group name HallP32"
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x-y,-y,-z
#5: -x,-x+y,-z
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11A-625-

HOH

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Components

#1: Protein Chloramphenicol acetyltransferase / CAT


Mass: 25448.650 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: cat / Production host: Escherichia coli (E. coli)
References: UniProt: P00485, chloramphenicol O-acetyltransferase
#2: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical
ChemComp-HEZ / HEXANE-1,6-DIOL


Mass: 118.174 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H14O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 264 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.81 Å3/Da / Density % sol: 56.27 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: CoCl2,CH3COONa,1,6-Hexanediol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: May 20, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→32.19 Å / Num. obs: 25985 / % possible obs: 97.3 % / Redundancy: 6.9 % / Biso Wilson estimate: 18.34 Å2 / Rmerge(I) obs: 0.045 / Χ2: 0.905 / Net I/σ(I): 15.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsDiffraction-ID% possible all
1.8-1.843.20.221345177.2
1.84-1.893.80.181547187
1.89-1.944.60.161665195.7
1.94-260.12917591100
2-2.067.60.1291786199.7
2.06-2.137.70.1081743199.8
2.13-2.227.70.0961779199.9
2.22-2.327.70.08117601100
2.32-2.447.80.07717801100
2.44-2.67.80.06717721100
2.6-2.87.80.05817741100
2.8-3.087.70.05318041100
3.08-3.527.70.04317931100
3.52-4.447.50.0418081100
4.44-32.197.10.0391870198.9

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHENIX1.19.1_4122refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3CLA

3cla


Resolution: 1.8→32.19 Å / SU ML: 0.1384 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.516
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.1662 1279 4.92 %Random selection
Rwork0.1505 24699 --
obs0.1513 25978 97.25 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.53 Å2
Refinement stepCycle: LAST / Resolution: 1.8→32.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1787 0 57 264 2108
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00661896
X-RAY DIFFRACTIONf_angle_d0.96712558
X-RAY DIFFRACTIONf_chiral_restr0.0515268
X-RAY DIFFRACTIONf_plane_restr0.0061324
X-RAY DIFFRACTIONf_dihedral_angle_d12.7627269
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.870.23451160.18172231X-RAY DIFFRACTION80.6
1.87-1.960.20091140.16082687X-RAY DIFFRACTION95.37
1.96-2.060.19181460.15972808X-RAY DIFFRACTION99.8
2.06-2.190.1791450.14562782X-RAY DIFFRACTION99.93
2.19-2.360.1511490.14432811X-RAY DIFFRACTION100
2.36-2.60.17721500.15412794X-RAY DIFFRACTION100
2.6-2.970.17161530.15052813X-RAY DIFFRACTION99.93
2.97-3.740.16451410.14432856X-RAY DIFFRACTION99.87
3.74-32.190.14461650.14942917X-RAY DIFFRACTION99.55

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