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- PDB-2i9d: chloramphenicol acetyltransferase -

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Basic information

Entry
Database: PDB / ID: 2i9d
Titlechloramphenicol acetyltransferase
ComponentsChloramphenicol acetyltransferase
KeywordsTRANSFERASE / chloramphenicol acetyltransferase / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


chloramphenicol O-acetyltransferase activity
Similarity search - Function
Chloramphenicol acetyltransferase / Chloramphenicol acetyltransferase / Chloramphenicol acetyltransferase / Chloramphenicol Acetyltransferase / Chloramphenicol acetyltransferase-like domain / Chloramphenicol acetyltransferase-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chloramphenicol acetyltransferase
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsDuke, N.E.C. / Li, H. / Abdullah, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: chloramphenicol acetyltransferase
Authors: Duke, N.E.C. / Li, H. / Abdullah, J. / Joachimiak, A.
History
DepositionSep 5, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version

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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


Theoretical massNumber of molelcules
Total (without water)75,5993
Polymers75,5993
Non-polymers00
Water3,891216
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5560 Å2
ΔGint-22 kcal/mol
Surface area25570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.144, 116.144, 130.863
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Chloramphenicol acetyltransferase /


Mass: 25199.785 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria)
Strain: VPI-5482 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 magic / References: UniProt: Q8A336
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 216 / 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: 3.37 Å3/Da / Density % sol: 63.49 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 60% v/v tacsimate 0.10 M bis-tris propane, pH 7.0 (Hampton Research SaltRx, reagent number 96, i.e. H12) , pH 7.00, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792896, 0.9794257
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 22, 2006
Details: double crystal monochromator sagittally focussing mirror
RadiationMonochromator: double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97928961
20.97942571
ReflectionRedundancy: 14.7 % / Av σ(I) over netI: 11.9 / Number: 653688 / Rmerge(I) obs: 0.093 / Χ2: 1.96 / D res high: 2.3 Å / D res low: 50 Å / Num. obs: 44553 / % possible obs: 100
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.955010010.0564.73414.4
3.934.9510010.0532.89414.9
3.443.9310010.0592.14215.1
3.123.4410010.0771.73515.1
2.93.1210010.1161.48315.2
2.732.910010.1721.35915.2
2.592.7310010.2421.30915.2
2.482.5910010.3171.2915
2.382.4810010.4211.28214.5
2.32.3810010.5141.29812.2
ReflectionResolution: 2.3→50 Å / Num. all: 44615 / Num. obs: 44581 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 / Redundancy: 14.6 % / Rmerge(I) obs: 0.104 / Χ2: 2.467 / Net I/σ(I): 11.6
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 12 % / Rmerge(I) obs: 0.524 / Num. unique all: 4406 / Χ2: 1.262 / % possible all: 99.5

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Phasing

PhasingMethod: MAD
Phasing MADD res high: 2.3 Å / D res low: 50 Å / FOM : 0.533 / FOM acentric: 0.535 / FOM centric: 0.45 / Reflection: 44392 / Reflection acentric: 43235 / Reflection centric: 1157
Phasing MAD set

Highest resolution: 2.3 Å / Lowest resolution: 50 Å / Reflection centric: 1157

IDR cullis acentricR cullis centricLoc acentricLoc centricPower acentricPower centricReflection acentric
12.4110.40.20043235
20.830.658.910.30.870.9843213
Phasing MAD set shell
IDResolution (Å)R cullis acentricR cullis centricLoc acentricLoc centricPower acentricPower centricReflection acentricReflection centric
113.92-502.211.20.60017930
18.08-13.921.4711.10.80078260
15.7-8.082.1210.90.400182596
14.4-5.71.4310.70.5003326128
13.58-4.41.3710.50.4005269161
13.02-3.582.0610.30.2007652194
12.61-3.026.7910.300010456226
12.3-2.6113.2710.200013746262
213.92-500.290.183.94.25.495.2517930
28.08-13.920.290.183.73.85.525.4778260
25.7-8.080.330.33.74.94.513.35182596
24.4-5.70.430.414.36.43.212.073326128
23.58-4.40.570.494.96.62.221.75269161
23.02-3.580.780.666.79.51.221.047652194
22.61-3.020.950.871013.40.590.5110449226
22.3-2.610.990.9713.116.50.330.2813731262
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Se24.049960.4210.6630.0210
2Se25.226150.4840.716-0.0610
3Se31.520710.4430.419-0.1310
4Se23.435420.6670.941-0.1730
5Se36.308550.480.53-0.1740
6Se23.754750.2360.5170.0420
7Se28.412230.7061.009-0.2560
8Se20.921870.2210.5410.0590
9Se32.528470.5350.496-0.10
10Se37.942980.6811.043-0.1680
11Se48.240860.4160.587-0.0280
12Se133.142270.7450.934-0.0320
13Se23.826050.4210.6630.021-0.105
14Se25.913070.4840.716-0.061-0.097
15Se33.580130.4430.419-0.131-0.1
16Se20.237660.6670.941-0.173-0.096
17Se37.408990.480.53-0.174-0.093
18Se24.289480.2360.5170.042-0.089
19Se28.132220.7061.008-0.256-0.09
20Se19.036160.2210.5410.059-0.084
21Se31.063090.5350.496-0.099-0.099
22Se36.146810.6811.043-0.168-0.094
23Se46.281150.4160.586-0.028-0.097
24Se131.100570.7440.933-0.032-0.053
Phasing MAD shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
13.92-500.9370.9550.83320917930
8.08-13.920.9370.9470.80384278260
5.7-8.080.9250.9340.7491921182596
4.4-5.70.8770.8850.65434543326128
3.58-4.40.8090.8160.58854305269161
3.02-3.580.6650.6690.50278467652194
2.61-3.020.4330.4360.2981068210456226
2.3-2.610.2590.2610.1251400813746262

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
RESOLVE2.08phasing
REFMACrefinement
PDB_EXTRACT2data extraction
SBC-Collectdata collection
HKL-3000data reduction
RefinementMethod to determine structure: MAD / Resolution: 2.3→43.44 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.924 / SU B: 5.419 / SU ML: 0.133 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.214 / ESU R Free: 0.188 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23 2264 5.1 %RANDOM
Rwork0.188 ---
all0.19 44615 --
obs-44491 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.208 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0.01 Å20 Å2
2---0.01 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.3→43.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4917 0 0 216 5133
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0225042
X-RAY DIFFRACTIONr_angle_refined_deg1.4851.9456812
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8575593
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.60623.321271
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.57715838
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8761539
X-RAY DIFFRACTIONr_chiral_restr0.1090.2715
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023939
X-RAY DIFFRACTIONr_nbd_refined0.2060.22211
X-RAY DIFFRACTIONr_nbtor_refined0.3080.23417
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.2269
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3450.257
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1170.212
X-RAY DIFFRACTIONr_mcbond_it1.1311.53083
X-RAY DIFFRACTIONr_mcangle_it1.59324807
X-RAY DIFFRACTIONr_scbond_it2.68632224
X-RAY DIFFRACTIONr_scangle_it3.7644.52005
LS refinement shellResolution: 2.3→2.357 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 166 -
Rwork0.245 3012 -
obs-3178 100 %

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