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- PDB-8tlb: Crystal structure of the peptidoglycan O-acetyltransferase B (Pat... -

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Basic information

Entry
Database: PDB / ID: 8tlb
TitleCrystal structure of the peptidoglycan O-acetyltransferase B (PatB) from Campylobacter jejuni, catalytic domain
ComponentsPeptidoglycan O-acetyltransferase B (PatB)
KeywordsTRANSFERASE / Peptidoglycan / O-acetyltransferase / DUF459 / SGNH hydrolase
Function / homology: / SGNH hydrolase superfamily / phosphatidylcholine lysophospholipase activity / DUF459 domain-containing protein
Function and homology information
Biological speciesCampylobacter jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsAnderson, A.C. / Malloch, T. / Clarke, A.J.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada) Canada
CitationJournal: To Be Published
Title: Structural basis for peptidoglycan O-acetylation in Gram-negative bacteria
Authors: Anderson, A.C. / Brott, A.S. / Stangherlin, S. / Malloch, T. / Clarke, A.J.
History
DepositionJul 26, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peptidoglycan O-acetyltransferase B (PatB)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2502
Polymers28,2141
Non-polymers351
Water1,856103
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.830, 55.830, 136.440
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Peptidoglycan O-acetyltransferase B (PatB)


Mass: 28214.172 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni (Campylobacter) / Strain: 81-176 / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C43
References: UniProt: A0A0H3PJC1, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / 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: 2.18 Å3/Da / Density % sol: 43.47 % / Description: Long and thin, needle-like hexagonal prismatic
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100 mM HEPES:NaOH pH 7.5, 200 mM NaCl, 25% (w/v) poly(ethylene glycol) 3500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.987 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 21, 2022
RadiationMonochromator: DOUBLE CRYSTAL MULTILAYER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.9→48.35 Å / Num. obs: 18944 / % possible obs: 99.98 % / Redundancy: 20.4 % / Biso Wilson estimate: 21.65 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.02244 / Rrim(I) all: 0.1012 / Net I/σ(I): 28.39
Reflection shellResolution: 1.9→1.968 Å / Redundancy: 21.4 % / Rmerge(I) obs: 0.7082 / Mean I/σ(I) obs: 9.23 / Num. unique obs: 1893 / CC1/2: 0.977 / CC star: 0.994 / Rpim(I) all: 0.1566 / Rrim(I) all: 0.7254 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
XDSdata scaling
PHASER1.14_3260phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→48.35 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 19.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2032 941 5.01 %
Rwork0.1627 --
obs0.1647 18789 99.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→48.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1753 0 1 103 1857
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061788
X-RAY DIFFRACTIONf_angle_d0.7662407
X-RAY DIFFRACTIONf_dihedral_angle_d2.8511079
X-RAY DIFFRACTIONf_chiral_restr0.053265
X-RAY DIFFRACTIONf_plane_restr0.005303
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-2.00020.21561360.16462490X-RAY DIFFRACTION97
2.0002-2.12550.21471290.16452507X-RAY DIFFRACTION98
2.1255-2.28960.24581340.15672549X-RAY DIFFRACTION100
2.2896-2.520.19771350.17222568X-RAY DIFFRACTION100
2.52-2.88460.2061340.17772561X-RAY DIFFRACTION100
2.8846-3.63410.19791360.17062578X-RAY DIFFRACTION100
3.6341-48.350.1911370.14912595X-RAY DIFFRACTION100

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