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

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Basic information

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


phosphatidylcholine lysophospholipase A1 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
Biological speciesNeisseria gonorrhoeae FA 1090 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.30003477218 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 15, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 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)25,6912
Polymers25,5951
Non-polymers961
Water3,675204
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)144.900, 144.900, 80.140
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-582-

HOH

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Components

#1: Protein Peptidoglycan O-acetyltransferase B


Mass: 25595.334 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-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 204 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.16 Å3/Da / Density % sol: 61.11 %
Crystal growTemperature: 296 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: 0.97949 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 14, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.19→41.83 Å / Num. obs: 78745 / % possible obs: 99.96 % / Redundancy: 10.5 % / Biso Wilson estimate: 16.932585492 Å2 / CC1/2: 0.999 / Net I/σ(I): 17.4
Reflection shellResolution: 1.19→1.22 Å / Mean I/σ(I) obs: 0.61 / Num. unique obs: 102048 / CC1/2: 0.203

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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: PDB ID 7TLV

7tlv


Resolution: 1.30003477218→41.8290270028 Å / SU ML: 0.145565745133 / Cross valid method: THROUGHOUT / σ(F): 1.34638024946 / Phase error: 18.2376304099
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.188628037446 3937 4.99968251953 %
Rwork0.166287530393 74808 -
obs0.167431382176 78745 99.9631858227 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.5363455938 Å2
Refinement stepCycle: LAST / Resolution: 1.30003477218→41.8290270028 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1770 0 5 204 1979
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004675050297931833
X-RAY DIFFRACTIONf_angle_d0.7638259576742480
X-RAY DIFFRACTIONf_chiral_restr0.0802385132082266
X-RAY DIFFRACTIONf_plane_restr0.00567902319908314
X-RAY DIFFRACTIONf_dihedral_angle_d2.771888330831130
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.30003477218-1.31590.3331725456861400.3275031140072661X-RAY DIFFRACTION99.7862486641
1.3159-1.33250.2742671205851410.2892718180422669X-RAY DIFFRACTION99.8223801066
1.3325-1.35010.3285266529911390.2697198088682639X-RAY DIFFRACTION99.964015833
1.3501-1.36860.2505137770351400.2542365291212650X-RAY DIFFRACTION99.9283667622
1.3686-1.38810.2849695386721370.2404707251932638X-RAY DIFFRACTION99.8920086393
1.3881-1.40890.2670854449441400.2196862882262658X-RAY DIFFRACTION99.7504456328
1.4089-1.43090.2542718496591400.2148212748562662X-RAY DIFFRACTION100
1.4309-1.45430.2438645086571390.2107452483852652X-RAY DIFFRACTION99.9283924096
1.4543-1.47940.2194664705131410.1975903167312667X-RAY DIFFRACTION99.9644001424
1.4794-1.50630.1972089876241400.1611268277292668X-RAY DIFFRACTION100
1.5063-1.53530.1759122332891390.1459751422462636X-RAY DIFFRACTION100
1.5353-1.56660.1867655370331410.143245238182672X-RAY DIFFRACTION99.9644633973
1.5666-1.60070.188903775391400.1427194045712673X-RAY DIFFRACTION100
1.6007-1.63790.1671155520051400.1384082269882662X-RAY DIFFRACTION100
1.6379-1.67890.184457761451400.133432104452647X-RAY DIFFRACTION100
1.6789-1.72430.1515641666961410.1338256764182682X-RAY DIFFRACTION100
1.7243-1.7750.1703177367631400.1374009017352655X-RAY DIFFRACTION100
1.775-1.83230.1521299628311410.1388217201872683X-RAY DIFFRACTION100
1.8323-1.89780.151511754751400.1404696090772652X-RAY DIFFRACTION100
1.8978-1.97380.1710268687141400.1467578654132664X-RAY DIFFRACTION100
1.9738-2.06360.1905144111541410.1538955489092691X-RAY DIFFRACTION100
2.0636-2.17240.1735346821461410.1552950454132665X-RAY DIFFRACTION100
2.1724-2.30850.1845453068791410.1592172201932693X-RAY DIFFRACTION100
2.3085-2.48670.1988793901681410.1676932667012679X-RAY DIFFRACTION100
2.4867-2.73690.2095377689911420.1788091087552690X-RAY DIFFRACTION100
2.7369-3.13290.2169558079141420.1785639110942700X-RAY DIFFRACTION100
3.1329-3.94660.1776867091391430.1605563683942713X-RAY DIFFRACTION100
3.9466-41.82902700280.1683622955931470.170095460742787X-RAY DIFFRACTION99.9659284497

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