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- PDB-3u9b: Structure of apo-CATI -

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Basic information

Entry
Database: PDB / ID: 3u9b
TitleStructure of apo-CATI
ComponentsChloramphenicol acetyltransferase
KeywordsTRANSFERASE / Chrolamphenicol resistance / 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: 3.2 Å
AuthorsBiswas, T. / Garneau-Tsodikova, S. / Tsodikov, O.V.
CitationJournal: Protein Sci. / Year: 2012
Title: The structural basis for substrate versatility of chloramphenicol acetyltransferase CAT(I).
Authors: Biswas, T. / Houghton, J.L. / Garneau-Tsodikova, S. / Tsodikov, O.V.
History
DepositionOct 18, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 29, 2012Group: Structure summary
Revision 1.2Apr 4, 2012Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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


Theoretical massNumber of molelcules
Total (without water)231,2299
Polymers231,2299
Non-polymers00
Water00
1
A: Chloramphenicol acetyltransferase
B: Chloramphenicol acetyltransferase
C: Chloramphenicol acetyltransferase


Theoretical massNumber of molelcules
Total (without water)77,0763
Polymers77,0763
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6140 Å2
ΔGint-33 kcal/mol
Surface area28750 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
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6280 Å2
ΔGint-35 kcal/mol
Surface area27510 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
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6250 Å2
ΔGint-36 kcal/mol
Surface area27870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.159, 102.743, 114.093
Angle α, β, γ (deg.)90.00, 119.94, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Chloramphenicol acetyltransferase / CAT


Mass: 25692.145 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: cat / Production host: Escherichia coli (E. coli)
References: UniProt: P62577, chloramphenicol O-acetyltransferase

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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: 2.53 Å3/Da / Density % sol: 51.37 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100 mM HEPES pH 7.5, 20% PEG 4000, isopropanol 10% v/v, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 18, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. all: 38684 / Num. obs: 38065 / % possible obs: 98.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→40 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.852 / SU B: 82.803 / SU ML: 0.583 / Cross valid method: THROUGHOUT / ESU R Free: 0.657 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.3009 1897 5 %RANDOM
Rwork0.23496 ---
obs0.23823 35818 98.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 77.93 Å2
Baniso -1Baniso -2Baniso -3
1--6.2 Å20 Å2-2.57 Å2
2--9.38 Å20 Å2
3----5.74 Å2
Refinement stepCycle: LAST / Resolution: 3.2→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15981 0 0 0 15981
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02216521
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.081.89822432
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.93951921
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.37624.141891
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.876152579
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9041545
X-RAY DIFFRACTIONr_chiral_restr0.0820.22307
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0213003
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2120.27700
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3110.211042
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1210.2402
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3430.293
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0450.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.2281.59838
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.365215582
X-RAY DIFFRACTIONr_scbond_it0.4637718
X-RAY DIFFRACTIONr_scangle_it0.5484.56850
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.2→3.283 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 118 -
Rwork0.306 2316 -
obs--86.96 %
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)
13.28430.4617-0.25191.6358-0.39573.4310.05550.21290.10310.07970.1414-0.2564-0.00220.3984-0.1968-0.29040.0342-0.0206-0.0342-0.0899-0.242146.204-0.069921.1042
23.88050.07090.24831.30230.81876.53430.0337-0.2261-0.04860.37530.19760.1470.0471-0.2789-0.2313-0.1180.05460.0249-0.63760.0911-0.190623.53280.115942.7132
32.60250.0153-0.15241.8422-0.34663.5138-0.14490.2420.059-0.14190.23920.18670.0558-0.6388-0.0943-0.2571-0.0334-0.00780.07810.0577-0.293116.0419-0.380912.2709
42.91890.25760.41191.870.75853.9091-0.04640.34130.2031-0.0511-0.01060.4153-0.1877-0.38640.057-0.33020.0173-0.02610.06690.0067-0.2027-46.36518.293654.5516
53.76050.3283-0.2312.3417-0.49114.1089-0.0774-0.18640.17760.25990.085-0.2519-0.21370.098-0.0076-0.28010.0151-0.0468-0.1148-0.0562-0.2605-23.350218.033175.3704
63.9496-1.08890.46862.3428-0.2572.79720.05230.57230.2707-0.519-0.1669-0.204-0.18410.34820.1146-0.1734-0.07430.07240.10960.0417-0.2941-16.762718.29645.1554
72.99060.25340.19242.53361.19624.40190.1999-0.4593-0.04990.4227-0.14130.04440.0696-0.3081-0.0586-0.2418-0.14810.04560.1336-0.0867-0.338827.996849.721225.6459
84.0003-1.01550.02282.32260.20412.93870.13020.22720.0977-0.1303-0.03210.1114-0.0293-0.2434-0.0981-0.2372-0.11440.00910.078-0.1376-0.29114.480149.674-2.5485
93.20620.0792-0.24583.2847-1.46293.12710.07180.3107-0.0696-0.0328-0.0288-0.2510.01930.1017-0.043-0.3356-0.0675-0.01650.0896-0.1489-0.280345.645649.65930.1118
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 217
2X-RAY DIFFRACTION2B2 - 217
3X-RAY DIFFRACTION3C2 - 217
4X-RAY DIFFRACTION4D5 - 217
5X-RAY DIFFRACTION5E5 - 217
6X-RAY DIFFRACTION6F6 - 217
7X-RAY DIFFRACTION7G4 - 217
8X-RAY DIFFRACTION8H2 - 217
9X-RAY DIFFRACTION9I4 - 217

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