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- PDB-9xc8: Crystal structure of Bacteroides uniformis O-acetyltransferase -

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Basic information

Entry
Database: PDB / ID: 9xc8
TitleCrystal structure of Bacteroides uniformis O-acetyltransferase
ComponentsChloramphenicol O-acetyltransferase
KeywordsTRANSFERASE / O-acetyltransferase
Function / homologyChloramphenicol acetyltransferase / Chloramphenicol acetyltransferase / Chloramphenicol acetyltransferase / chloramphenicol O-acetyltransferase activity / Chloramphenicol acetyltransferase-like domain superfamily / Chloramphenicol O-acetyltransferase
Function and homology information
Biological speciesBacteroides uniformis dnLKV2 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59 Å
AuthorsMeng, C.Y. / Jian, X. / Wu, B.X.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structure of Bacteroides uniformis O-acetyltransferase
Authors: Meng, C.Y. / Jian, X. / Wu, B.X.
History
DepositionOct 25, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 12, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Chloramphenicol O-acetyltransferase
B: Chloramphenicol O-acetyltransferase
C: Chloramphenicol O-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,1016
Polymers75,7003
Non-polymers4013
Water12,953719
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)93.234, 117.923, 131.459
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11B-631-

HOH

21B-635-

HOH

31C-513-

HOH

41C-551-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 1 through 122 or (resid 123...
d_2ens_1(chain "B" and (resid 1 through 12 or (resid 13...
d_3ens_1(chain "C" and (resid 1 through 12 or (resid 13...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11METMETTHRTHRAA1 - 2032 - 204
d_12PHEPHESERSERAA205 - 217206 - 218
d_21METMETGLYGLYBB1 - 932 - 94
d_22PHEPHETHRTHRBB96 - 20397 - 204
d_23PHEPHESERSERBB205 - 217206 - 218
d_31METMETGLYGLYCC1 - 932 - 94
d_32PHEPHETHRTHRCC96 - 20397 - 204
d_33PHEPHESERSERCC205 - 217206 - 218

NCS oper:
IDCodeMatrixVector
1given(0.307662070008, 0.57207531548, -0.760311701934), (-0.618334811908, -0.487130264692, -0.616738328307), (-0.723191614347, 0.659874183947, 0.203862576996)-5.75258665412, -70.3318320075, -3.7508614329
2given(0.280357036874, -0.635091555027, -0.719762911387), (0.609020892225, -0.461897423834, 0.644782383979), (-0.741952481436, -0.619119929084, 0.257287832401)-45.7049277767, -27.5657262205, -46.1592591552

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Components

#1: Protein Chloramphenicol O-acetyltransferase


Mass: 25233.365 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: The first residue serine is from tag
Source: (gene. exp.) Bacteroides uniformis dnLKV2 (bacteria)
Gene: C801_01421 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: R9HWB4
#2: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


Mass: 209.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 719 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.39 Å3/Da / Density % sol: 48.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M BIS-TRIS pH 6.5, 25% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97861 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 21, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97861 Å / Relative weight: 1
ReflectionResolution: 1.59→30 Å / Num. obs: 96335 / % possible obs: 99.7 % / Redundancy: 13 % / Biso Wilson estimate: 22.41 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.019 / Rrim(I) all: 0.068 / Net I/σ(I): 22.3
Reflection shellResolution: 1.59→1.68 Å / Redundancy: 13.2 % / Rmerge(I) obs: 0.981 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 13894 / CC1/2: 0.863 / Rpim(I) all: 0.277 / Rrim(I) all: 1.021 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX1.21rc1_5156refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.59→29.98 Å / SU ML: 0.2012 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.8509
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2094 4867 5.05 %
Rwork0.1885 91420 -
obs0.1896 96287 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.07 Å2
Refinement stepCycle: LAST / Resolution: 1.59→29.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5199 0 24 719 5942
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00615375
X-RAY DIFFRACTIONf_angle_d0.87727305
X-RAY DIFFRACTIONf_chiral_restr0.0585779
X-RAY DIFFRACTIONf_plane_restr0.0081936
X-RAY DIFFRACTIONf_dihedral_angle_d12.86561888
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.768068308827
ens_1d_3AAX-RAY DIFFRACTIONTorsion NCS0.928015923932
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.59-1.610.3231740.32152925X-RAY DIFFRACTION97.45
1.61-1.630.3041630.28683016X-RAY DIFFRACTION99.94
1.63-1.650.341600.27983019X-RAY DIFFRACTION99.94
1.65-1.670.27781680.26373038X-RAY DIFFRACTION99.88
1.67-1.690.29051540.24353000X-RAY DIFFRACTION99.84
1.69-1.720.29221460.24443048X-RAY DIFFRACTION99.87
1.72-1.740.26591570.22443043X-RAY DIFFRACTION99.81
1.74-1.770.25991730.21893006X-RAY DIFFRACTION99.62
1.77-1.790.25961500.21923025X-RAY DIFFRACTION99.31
1.79-1.820.24351390.21773062X-RAY DIFFRACTION100
1.82-1.850.24911630.22033008X-RAY DIFFRACTION100
1.85-1.890.25051680.22383035X-RAY DIFFRACTION99.97
1.89-1.920.24391660.22713043X-RAY DIFFRACTION99.91
1.92-1.960.31641530.21513037X-RAY DIFFRACTION99.91
1.96-2.010.25761460.20273035X-RAY DIFFRACTION99.91
2.01-2.050.18521480.20283065X-RAY DIFFRACTION99.81
2.05-2.10.24721620.20133056X-RAY DIFFRACTION99.51
2.1-2.160.21351610.19883007X-RAY DIFFRACTION99.44
2.16-2.230.20051610.19543060X-RAY DIFFRACTION100
2.23-2.30.22511610.1963057X-RAY DIFFRACTION99.91
2.3-2.380.23661760.20633015X-RAY DIFFRACTION99.97
2.38-2.470.22981790.18973045X-RAY DIFFRACTION99.91
2.47-2.590.2451650.18973077X-RAY DIFFRACTION99.94
2.59-2.720.20571360.19073047X-RAY DIFFRACTION99.38
2.72-2.890.22121790.20133063X-RAY DIFFRACTION99.57
2.89-3.120.20661520.18653091X-RAY DIFFRACTION100
3.12-3.430.17231850.17463067X-RAY DIFFRACTION99.88
3.43-3.930.16431650.15553106X-RAY DIFFRACTION99.94
3.93-4.940.16441590.14073122X-RAY DIFFRACTION99.61
4.94-29.980.18311980.17643202X-RAY DIFFRACTION99.33

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