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- PDB-7trr: Structure of Neisseria gonorrhoeae peptidoglycan O-acetyltransfer... -

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Basic information

Entry
Database: PDB / ID: 7trr
TitleStructure of Neisseria gonorrhoeae peptidoglycan O-acetyltransferase B (PatB) with methylsulfonyl adduct
ComponentsPeptidoglycan O-acetyltransferase B
KeywordsTRANSFERASE / Peptidoglycan / O-acetyltransferase / Neisseria / gonorrhoeae
Function / homology
Function and homology information


phosphatidylcholine lysophospholipase activity
Similarity search - Function
Protein of unknown function DUF459 / Protein of unknown function (DUF459) / : / SGNH hydrolase / SGNH hydrolase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
methanesulfonic acid / Periplasmic protein
Similarity search - Component
Biological speciesNeisseria gonorrhoeae FA 1090 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8000158121 Å
AuthorsBrott, A.S. / Stangherlin, S. / Clarke, A.J.
Funding support Canada, 2items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)PJT156353 Canada
Canadian Glycomics Network (GLYCONET) Canada
CitationJournal: To Be Published
Title: Structure of Neisseria gonorrhoeae peptidoglycan O-acetyltransferase B (PatB)
Authors: Brott, A.S. / Stangherlin, S. / Clarke, A.J.
History
DepositionJan 30, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 1, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Peptidoglycan O-acetyltransferase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5332
Polymers25,4371
Non-polymers961
Water2,378132
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)145.680, 145.680, 78.410
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Space group name HallR32"
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x-y,-y,-z
#5: -x,-x+y,-z
#6: y,x,-z
#7: x+1/3,y+2/3,z+2/3
#8: -y+1/3,x-y+2/3,z+2/3
#9: -x+y+1/3,-x+2/3,z+2/3
#10: x-y+1/3,-y+2/3,-z+2/3
#11: -x+1/3,-x+y+2/3,-z+2/3
#12: y+1/3,x+2/3,-z+2/3
#13: x+2/3,y+1/3,z+1/3
#14: -y+2/3,x-y+1/3,z+1/3
#15: -x+y+2/3,-x+1/3,z+1/3
#16: x-y+2/3,-y+1/3,-z+1/3
#17: -x+2/3,-x+y+1/3,-z+1/3
#18: y+2/3,x+1/3,-z+1/3
Components on special symmetry positions
IDModelComponents
11A-520-

HOH

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Components

#1: Protein Peptidoglycan O-acetyltransferase B / Periplasmic protein


Mass: 25437.178 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria gonorrhoeae FA 1090 (bacteria)
Strain: ATCC 700825 / FA 1090 / Gene: NGO_0533 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: Q5F966
#2: Chemical ChemComp-03S / methanesulfonic acid


Mass: 96.106 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH4O3S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / 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: 3.15 Å3/Da / Density % sol: 60.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 2.08 M ammonium sulfate in 0.1 M phosphate-citrate buffer

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97828 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97828 Å / Relative weight: 1
ReflectionResolution: 1.41997→72.85 Å / Num. obs: 58729 / % possible obs: 100 % / Redundancy: 32 % / Biso Wilson estimate: 22.70018156 Å2 / CC1/2: 0.996 / Net I/σ(I): 2.8
Reflection shellResolution: 1.43→1.47 Å / Num. unique obs: 4786 / CC1/2: 0.44

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7TLV

7tlv


Resolution: 1.8000158121→49.1500006166 Å / SU ML: 0.210577724527 / Cross valid method: THROUGHOUT / σ(F): 1.36300540135 / Phase error: 23.437185808
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.229270406311 1007 3.4074374852 %
Rwork0.195887708069 28546 -
obs0.197007674053 29553 99.9864668268 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.2026547367 Å2
Refinement stepCycle: LAST / Resolution: 1.8000158121→49.1500006166 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1752 0 0 132 1884
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006253227225921802
X-RAY DIFFRACTIONf_angle_d0.7112005670862429
X-RAY DIFFRACTIONf_chiral_restr0.056917609328259
X-RAY DIFFRACTIONf_plane_restr0.00524198936351307
X-RAY DIFFRACTIONf_dihedral_angle_d14.03116132411082
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8000158121-1.89490.2967524557621420.2480170733484022X-RAY DIFFRACTION99.9519923188
1.8949-2.01360.2480778337461420.2073389151064044X-RAY DIFFRACTION100
2.0136-2.16910.2333131060491440.2006151534044053X-RAY DIFFRACTION100
2.1691-2.38740.2273721632341430.1944770723074066X-RAY DIFFRACTION100
2.3874-2.73280.2294318328571440.2000448440974070X-RAY DIFFRACTION99.9762752076
2.7328-3.4430.2473103041671440.1950763682394102X-RAY DIFFRACTION100
3.443-49.15000061660.2068757880111480.1854211783224189X-RAY DIFFRACTION100

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