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- PDB-3eev: Crystal Structure of Chloramphenicol Acetyltransferase VCA0300 fr... -

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Basic information

Entry
Database: PDB / ID: 3eev
TitleCrystal Structure of Chloramphenicol Acetyltransferase VCA0300 from Vibrio cholerae O1 biovar eltor
ComponentsChloramphenicol acetyltransferase
KeywordsTRANSFERASE / beta-helix / structural genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


chloramphenicol O-acetyltransferase / acyltransferase activity / response to antibiotic
Similarity search - Function
: / Hexapeptide transferase, conserved site / Hexapeptide-repeat containing-transferases signature. / 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 acetyltransferase
Similarity search - Component
Biological speciesVibrio cholerae O1 biovar El Tor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.61 Å
AuthorsKim, Y. / Maltseva, N. / Kwon, K. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: Crystal Structure of Chloramphenicol Acetyltransferase VCA0300 from Vibrio cholerae O1 biovar eltor
Authors: Kim, Y. / Maltseva, N. / Kwon, K. / Anderson, W.F. / Joachimiak, A.
History
DepositionSep 5, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 16, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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: Chloramphenicol acetyltransferase
B: Chloramphenicol acetyltransferase
C: Chloramphenicol acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,8926
Polymers71,5373
Non-polymers3553
Water3,927218
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10880 Å2
ΔGint-86 kcal/mol
Surface area25220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.972, 99.972, 127.374
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11B-300-

HOH

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Components

#1: Protein Chloramphenicol acetyltransferase


Mass: 23845.730 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae O1 biovar El Tor (bacteria)
Strain: N16961 / Gene: catB9, VC_A0300 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 / References: UniProt: Q9KMN1
#2: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 218 / 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: 2.57 Å3/Da / Density % sol: 52.11 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M Ammonium phosphate, 0.1 M TRIS pH 8.5, 50 %v/v MPD, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9793 Å
DetectorType: SBC-3 / Detector: CCD / Date: Aug 11, 2008 / Details: mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.6→32.7 Å / Num. all: 22994 / Num. obs: 22994 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.7 % / Biso Wilson estimate: 48.67 Å2 / Rmerge(I) obs: 0.103 / Net I/σ(I): 5.1
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 9.1 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 2.5 / Num. unique all: 1129 / % possible all: 99.6

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
BALBESphasing
REFMAC5.5.0053refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2xat

2xat


Resolution: 2.61→32.7 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.93 / SU B: 22.715 / SU ML: 0.219 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.027 / ESU R Free: 0.314 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.242 1177 5.1 %RANDOM
Rwork0.175 ---
all0.178 21757 --
obs0.178 21757 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.618 Å2
Baniso -1Baniso -2Baniso -3
1--1.09 Å2-0.54 Å20 Å2
2---1.09 Å20 Å2
3---1.63 Å2
Refinement stepCycle: LAST / Resolution: 2.61→32.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4926 0 24 218 5168
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0215109
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6061.9156938
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3665619
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.38123.815249
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.26115783
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5941523
X-RAY DIFFRACTIONr_chiral_restr0.1130.2708
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213990
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6821.53076
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.32224957
X-RAY DIFFRACTIONr_scbond_it2.26132033
X-RAY DIFFRACTIONr_scangle_it3.5784.51981
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.61→2.673 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.351 98 -
Rwork0.23 1558 -
obs-1656 99.16 %
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)
10.28170.01410.20971.2338-0.24640.2439-0.0053-0.02730.08030.0905-0.00360.0873-0.0330.00970.00890.0216-0.01360.00390.0404-0.01090.1128-45.916134.8481.5936
20.90180.46930.07071.05160.05360.4799-0.01920.02960.03870.06490.05990.26880.0394-0.0457-0.04060.0107-0.00050.01810.018-0.01020.1789-72.697420.14722.8609
30.69520.0199-0.03370.56010.09690.43370.0113-0.0914-0.06490.0484-0.01170.07850.00840.010.00050.027-0.00450.00450.01520.00060.1055-46.65984.0571-0.9053
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 2085 - 211
2X-RAY DIFFRACTION2BB1 - 2054 - 208
3X-RAY DIFFRACTION3CC1 - 2084 - 211

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