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- PDB-6u9c: The 2.2 A Crystal Structure of the Type B Chloramphenicol Acetylt... -

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Basic information

Entry
Database: PDB / ID: 6u9c
TitleThe 2.2 A Crystal Structure of the Type B Chloramphenicol Acetyltransferase from Vibrio cholerae in the complex with Acetyl CoA
ComponentsChloramphenicol acetyltransferase
KeywordsTRANSFERASE / left-handed beta helix / hexapeptide repeats / 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 proteins / UDP N-Acetylglucosamine Acyltransferase; domain 1 / Hexapeptide repeat / Bacterial transferase hexapeptide (six repeats) / Trimeric LpxA-like superfamily / 3 Solenoid / Mainly Beta
Similarity search - Domain/homology
ACETYL COENZYME *A / CITRIC ACID / ISOPROPYL ALCOHOL / Chloramphenicol acetyltransferase
Similarity search - Component
Biological speciesVibrio cholerae serotype O1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsKim, Y. / Maltseva, N. / Stam, J. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: To Be Published
Title: The 2.2 A Crystal Structure of the Type B Chloramphenicol Acetyltransferase from Vibrio cholerae in the complex with Acetyl CoA
Authors: Kim, Y. / Maltseva, N. / Stam, J. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionSep 7, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,73314
Polymers71,5373
Non-polymers3,19611
Water64936
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12930 Å2
ΔGint-56 kcal/mol
Surface area26470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.231, 101.231, 126.184
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

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Components

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Protein , 1 types, 3 molecules ABC

#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 serotype O1 (strain ATCC 39315 / El Tor Inaba N16961) (bacteria)
Strain: ATCC 39315 / El Tor Inaba N16961 / Gene: VC_A0300 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9KMN1

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Non-polymers , 6 types, 47 molecules

#2: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-ACO / ACETYL COENZYME *A / Acetyl-CoA


Mass: 809.571 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C23H38N7O17P3S / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL / Isopropyl alcohol


Mass: 60.095 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.61 Å3/Da / Density % sol: 52.87 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M tri-Sodium citrate 20 %(w/v) PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Aug 20, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.2→47 Å / Num. obs: 37660 / % possible obs: 97.9 % / Redundancy: 10.2 % / Biso Wilson estimate: 48.7 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 20.4
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 9.7 % / Rmerge(I) obs: 0.667 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 1509 / CC1/2: 0.925 / % possible all: 80.2

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDBID 3EEV

3eev


Resolution: 2.2→46.98 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 33.43
RfactorNum. reflection% reflection
Rfree0.2507 1753 4.67 %
Rwork0.2061 --
obs0.2082 37576 97.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 70.9 Å2
Refinement stepCycle: LAST / Resolution: 2.2→46.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4951 0 168 36 5155
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075270
X-RAY DIFFRACTIONf_angle_d0.9167180
X-RAY DIFFRACTIONf_chiral_restr0.059727
X-RAY DIFFRACTIONf_plane_restr0.005908
X-RAY DIFFRACTIONf_dihedral_angle_d16.5152987
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.260.27851070.28222296X-RAY DIFFRACTION83
2.26-2.330.29981420.2852537X-RAY DIFFRACTION92
2.33-2.40.34361300.27462731X-RAY DIFFRACTION97
2.4-2.490.33821540.26722729X-RAY DIFFRACTION99
2.49-2.590.35951140.2692805X-RAY DIFFRACTION100
2.59-2.710.33021390.25842796X-RAY DIFFRACTION100
2.71-2.850.36371150.25312814X-RAY DIFFRACTION100
2.85-3.030.28141370.25852791X-RAY DIFFRACTION100
3.03-3.260.31831660.24382801X-RAY DIFFRACTION100
3.26-3.590.23981450.20772812X-RAY DIFFRACTION100
3.59-4.110.20191280.17882845X-RAY DIFFRACTION100
4.11-5.170.18851260.15592880X-RAY DIFFRACTION100
5.17-46.980.22631500.1852986X-RAY DIFFRACTION100
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)
19.54744.2981-0.49583.67142.48464.35780.5298-0.99450.3226-0.2139-0.89990.67880.1472-0.51810.31080.85230.04320.07410.7616-0.12110.5021-57.5732.69217.8091
23.6076-1.4166-0.23763.3129-1.51792.0792-0.2003-0.87790.22760.86680.24010.1307-0.0978-0.1733-0.00880.62520.0064-0.02390.5129-0.02130.3081-48.691634.088712.698
32.2818-3.8246-1.6256.02222.03591.1652-0.052-0.10560.21040.56730.0735-0.58410.1683-0.0005-0.02020.5958-0.0106-0.06280.52940.02260.4666-38.821825.33483.5831
44.4627-5.1611.65576.296-0.97184.28040.10540.07740.58830.4597-0.1857-1.29190.35190.47460.10450.5731-0.0684-0.04270.6606-0.05650.592-27.820814.06313.0707
52.05890.20191.11892.9050.23060.7257-0.05590.2155-0.0415-0.34310.05850.12490.0479-0.0087-0.00090.50130.0258-0.01310.490.01040.3657-50.184733.0615-3.5569
64.40430.05611.61559.89713.33594.0678-0.2670.5389-0.2681-0.830.22620.5248-0.2870.0115-0.04060.46550.00170.04440.5380.04890.4086-53.802445.5206-11.0895
76.07182.9198-0.09055.41951.4082.8384-0.25190.00020.9080.0455-0.14160.6408-0.03650.0690.3570.50230.0542-0.0330.5481-0.01320.5944-54.634755.34962.5999
85.74624.99334.76864.61345.09628.2668-0.57540.12951.2231-1.4342-0.23960.9944-0.5954-0.13590.77630.6630.0274-0.16540.55410.0570.6855-52.599261.7535-6.3259
91.3017-1.10260.98831.3726-0.76030.8487-0.8862-0.4156-0.99260.17070.08591.1170.0553-0.630.49011.0848-0.17620.4721.04530.02111.018-66.40238.618315.999
105.3246-3.45140.38815.41851.23562.4014-0.2174-0.53760.63030.98610.35370.3650.75580.2146-0.15190.9279-0.04480.38340.9473-0.07860.9959-77.024920.819414.2063
117.0729-0.9669-0.76422.5047-1.52634.5419-0.0673-0.32820.30271.06780.17891.242-0.2433-0.3774-0.21150.6486-0.00160.27520.5913-0.08150.8805-70.79422.424511.4739
120.81820.3199-0.37885.3389-0.71350.2552-0.0284-0.2646-0.18830.2213-0.22681.54690.1018-0.17620.24570.5550.00380.10240.5474-0.05840.8456-67.480730.6783.2674
136.67533.83230.34142.77781.35145.14440.2291-0.7163-0.28650.3293-0.54340.9747-0.2764-0.15040.38510.63610.07030.16240.6591-0.0330.6473-64.873146.21017.9934
142.96782.26611.66252.26810.13792.06160.15530.1554-0.6188-0.27380.05941.66530.1238-0.3188-0.20670.4949-0.0198-0.13450.5502-0.13751.2211-73.336716.6455-6.4012
152.53341.1918-2.8310.9759-2.72417.97890.32330.357-0.29610.27851.30411.50680.361-1.632-0.84840.6129-0.40050.41881.015-0.14732.9434-89.61337.23722.2077
167.11181.9832-2.57858.4955.32828.6947-1.21810.2738-0.2438-0.24130.41120.64540.24370.34720.38190.6802-0.0641-0.18820.6789-0.0082.5155-84.8278-1.6366-1.9677
172.7663-3.47960.37114.66720.70264.75930.13951.0532-0.1325-0.1125-0.22960.62221.2658-1.2621-0.16341.0081-0.3321-0.75941.21570.13292.3273-92.48312.8386-9.2504
183.2844-1.6521-0.53673.88460.54453.5756-0.212-0.6002-0.43110.78880.04910.39410.1425-0.11530.10810.63060.00840.09480.55050.0560.4627-47.93754.97358.5688
197.58810.1286-0.01818.0664-2.70196.2158-0.4135-0.3036-1.48390.39040.27741.04290.273-1.21130.34360.5913-0.06860.06280.729-0.02311.4369-75.91882.04262.9563
203.4484-1.6509-1.70920.87060.62891.94580.0751-0.0346-0.5894-0.0927-0.02730.3844-0.0255-0.0475-0.07770.49220.0089-0.04480.4426-0.06630.5106-51.13526.7787-6.1375
215.8908-1.59460.41124.5726-1.81625.7080.0978-0.3585-0.57950.05080.0117-0.25680.31080.20950.00960.4305-0.03160.03450.4025-0.03370.4169-26.8607-0.3623-9.5728
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'C' and (resid 1 through 12 )
2X-RAY DIFFRACTION2chain 'C' and (resid 13 through 42 )
3X-RAY DIFFRACTION3chain 'C' and (resid 43 through 87 )
4X-RAY DIFFRACTION4chain 'C' and (resid 88 through 108 )
5X-RAY DIFFRACTION5chain 'C' and (resid 109 through 156 )
6X-RAY DIFFRACTION6chain 'C' and (resid 157 through 174 )
7X-RAY DIFFRACTION7chain 'C' and (resid 175 through 195 )
8X-RAY DIFFRACTION8chain 'C' and (resid 196 through 209 )
9X-RAY DIFFRACTION9chain 'A' and (resid 1 through 12 )
10X-RAY DIFFRACTION10chain 'A' and (resid 13 through 24 )
11X-RAY DIFFRACTION11chain 'A' and (resid 25 through 55 )
12X-RAY DIFFRACTION12chain 'A' and (resid 56 through 87 )
13X-RAY DIFFRACTION13chain 'A' and (resid 88 through 108 )
14X-RAY DIFFRACTION14chain 'A' and (resid 109 through 174 )
15X-RAY DIFFRACTION15chain 'A' and (resid 175 through 184 )
16X-RAY DIFFRACTION16chain 'A' and (resid 185 through 195 )
17X-RAY DIFFRACTION17chain 'A' and (resid 196 through 206 )
18X-RAY DIFFRACTION18chain 'B' and (resid 1 through 73 )
19X-RAY DIFFRACTION19chain 'B' and (resid 74 through 96 )
20X-RAY DIFFRACTION20chain 'B' and (resid 97 through 164 )
21X-RAY DIFFRACTION21chain 'B' and (resid 165 through 209 )

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