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- PDB-8j40: Crystal Structure of CATB8 in complex with chloramphenicol -

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Basic information

Entry
Database: PDB / ID: 8j40
TitleCrystal Structure of CATB8 in complex with chloramphenicol
ComponentsCatB8
KeywordsTRANSFERASE / Antibiotic resistance
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 / Bacterial transferase hexapeptide (six repeats) / Trimeric LpxA-like superfamily
Similarity search - Domain/homology
CHLORAMPHENICOL / Chloramphenicol acetyltransferase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 Å
AuthorsLiao, J. / Kuang, L. / Jiang, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)2019YJ0083 China
CitationJournal: Acs Infect Dis. / Year: 2024
Title: Chloramphenicol Binding Sites of Acinetobacter baumannii Chloramphenicol Acetyltransferase CatB8.
Authors: Liao, J. / Qi, Q. / Kuang, L. / Zhou, Y. / Xiao, Q. / Liu, T. / Wang, X. / Guo, L. / Jiang, Y.
History
DepositionApr 18, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Feb 28, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CatB8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,67310
Polymers24,9161
Non-polymers1,7579
Water5,585310
1
A: CatB8
hetero molecules

A: CatB8
hetero molecules

A: CatB8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,02030
Polymers74,7493
Non-polymers5,27127
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area20660 Å2
ΔGint-237 kcal/mol
Surface area23300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.548, 128.548, 128.548
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number197
Space group name H-MI23
Space group name HallI223
Symmetry operation#1: x,y,z
#2: z,x,y
#3: y,z,x
#4: -y,-z,x
#5: z,-x,-y
#6: -y,z,-x
#7: -z,-x,y
#8: -z,x,-y
#9: y,-z,-x
#10: x,-y,-z
#11: -x,y,-z
#12: -x,-y,z
#13: x+1/2,y+1/2,z+1/2
#14: z+1/2,x+1/2,y+1/2
#15: y+1/2,z+1/2,x+1/2
#16: -y+1/2,-z+1/2,x+1/2
#17: z+1/2,-x+1/2,-y+1/2
#18: -y+1/2,z+1/2,-x+1/2
#19: -z+1/2,-x+1/2,y+1/2
#20: -z+1/2,x+1/2,-y+1/2
#21: y+1/2,-z+1/2,-x+1/2
#22: x+1/2,-y+1/2,-z+1/2
#23: -x+1/2,y+1/2,-z+1/2
#24: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-538-

HOH

21A-615-

HOH

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Components

#1: Protein CatB8 / Chloramphenicol acetyltransferase


Mass: 24916.232 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: catB8
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q6Q627
#2: Chemical
ChemComp-CLM / CHLORAMPHENICOL


Mass: 323.129 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H12Cl2N2O5 / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic*YM
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 310 / Source method: isolated from a natural source / Formula: H2O
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: 3.74 Å3/Da / Density % sol: 64 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 1.5 M Ammonium sulfate + 0.1 M Tris pH 8.5 + 12% v/v Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 13, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.57→50 Å / Num. obs: 49090 / % possible obs: 99.9 % / Redundancy: 19 % / Biso Wilson estimate: 17.93 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.14 / Net I/σ(I): 40
Reflection shellResolution: 1.57→1.6 Å / Rmerge(I) obs: 0.671 / Mean I/σ(I) obs: 2 / Num. unique obs: 2318 / CC1/2: 0.888 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.57→30.3 Å / SU ML: 0.1019 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 16.1134
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1633 1986 4.05 %
Rwork0.1561 47072 -
obs0.1564 49058 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.74 Å2
Refinement stepCycle: LAST / Resolution: 1.57→30.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1671 0 109 310 2090
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00871834
X-RAY DIFFRACTIONf_angle_d1.07792473
X-RAY DIFFRACTIONf_chiral_restr0.0676241
X-RAY DIFFRACTIONf_plane_restr0.0101316
X-RAY DIFFRACTIONf_dihedral_angle_d8.3775241
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.57-1.610.19261390.16333329X-RAY DIFFRACTION99.8
1.61-1.650.171420.16083314X-RAY DIFFRACTION100
1.65-1.70.1761410.16113343X-RAY DIFFRACTION100
1.7-1.760.18861410.17743341X-RAY DIFFRACTION100
1.76-1.820.18621430.18643364X-RAY DIFFRACTION99.97
1.82-1.890.18031400.16183348X-RAY DIFFRACTION100
1.89-1.980.17241410.15943321X-RAY DIFFRACTION100
1.98-2.080.16551400.14683380X-RAY DIFFRACTION100
2.08-2.210.18011450.15533342X-RAY DIFFRACTION100
2.22-2.390.14831430.15133363X-RAY DIFFRACTION100
2.39-2.630.17211390.16113374X-RAY DIFFRACTION100
2.63-30.17951440.15533389X-RAY DIFFRACTION100
3.01-3.780.13171440.15153411X-RAY DIFFRACTION100
3.79-30.30.16051440.15123453X-RAY DIFFRACTION99.15
Refinement TLS params.Method: refined / Origin x: 22.306668641 Å / Origin y: 11.9272149088 Å / Origin z: 37.0030708508 Å
111213212223313233
T0.136293300924 Å2-0.00108627679162 Å20.00325001368218 Å2-0.130697054244 Å20.0146625014386 Å2--0.146883246356 Å2
L0.243354344463 °2-0.123766130899 °20.0549221429056 °2-0.358248505791 °2-0.185293952209 °2--0.446598683572 °2
S-0.00737449255059 Å °-0.0627352341857 Å °-0.0402960900193 Å °0.00644223880301 Å °-0.00685638377556 Å °-0.00233168288805 Å °0.0187641284996 Å °-0.00163251963662 Å °0.00128819577145 Å °
Refinement TLS groupSelection details: all

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