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

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Basic information

Entry
Database: PDB / ID: 7tlv
TitleStructure of Neisseria gonorrhoeae peptidoglycan O-acetyltransferase B (PatB) substituted with selenomethionine
ComponentsPeriplasmic protein
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 / SAD / Resolution: 1.50000733668 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 18, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Periplasmic protein


Theoretical massNumber of molelcules
Total (without water)25,7831
Polymers25,7831
Non-polymers00
Water2,720151
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)145.170, 145.170, 79.090
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-439-

HOH

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Components

#1: Protein Periplasmic protein


Mass: 25782.912 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 (E. coli) / Strain (production host): B834 (DE3) / References: UniProt: Q5F966
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 3.11 Å3/Da / Density % sol: 60.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: The 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 PILATUS3 S 6M / Detector: PIXEL / Date: Jan 31, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97828 Å / Relative weight: 1
ReflectionResolution: 1.2→49.2104303455 Å / Num. obs: 485015 / % possible obs: 99.03 % / Redundancy: 6.1 % / Biso Wilson estimate: 16.214214437 Å2 / CC1/2: 0.998 / Net I/σ(I): 9.84
Reflection shellResolution: 1.2→1.24 Å / Num. unique obs: 79513 / CC1/2: 0.091

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.50000733668→49.2104303455 Å / SU ML: 0.183624239553 / Cross valid method: THROUGHOUT / σ(F): 1.81791212427 / Phase error: 22.727811104
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.221617100583 4926 4.99797077922 %
Rwork0.203687736463 93634 -
obs0.204577890638 98560 99.0284043526 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.9222524389 Å2
Refinement stepCycle: LAST / Resolution: 1.50000733668→49.2104303455 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1746 0 0 151 1897
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006400135126411805
X-RAY DIFFRACTIONf_angle_d0.8052048828972442
X-RAY DIFFRACTIONf_chiral_restr0.0601109731488263
X-RAY DIFFRACTIONf_plane_restr0.00551266685103309
X-RAY DIFFRACTIONf_dihedral_angle_d12.4656316652682
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.50000733668-1.51710.3298425124991650.3226185645033120X-RAY DIFFRACTION100
1.5171-1.53490.3153108947041660.3171948842893110X-RAY DIFFRACTION99.9389871873
1.5349-1.55360.2993829529631660.2745393604333170X-RAY DIFFRACTION99.8503442083
1.5536-1.57330.2998641284311680.2869844839823149X-RAY DIFFRACTION100
1.5733-1.5940.2787692973151680.2683612155513179X-RAY DIFFRACTION99.9701314217
1.594-1.61580.2728792758651640.2537296260373141X-RAY DIFFRACTION99.9093107618
1.6158-1.63890.2881345945311620.2447824317893128X-RAY DIFFRACTION100
1.6389-1.66340.267997585821660.2341585274533163X-RAY DIFFRACTION99.850029994
1.6634-1.68940.253706627591680.230513511633170X-RAY DIFFRACTION99.9401197605
1.6894-1.71710.2761304324171610.2284574739853122X-RAY DIFFRACTION100
1.7171-1.74670.2553011937341630.2263508051793141X-RAY DIFFRACTION99.8488969477
1.7467-1.77840.2862607151851660.218346715543168X-RAY DIFFRACTION99.8502545672
1.7784-1.81270.2301042133931640.2153500155953118X-RAY DIFFRACTION99.7871693524
1.8127-1.84970.2204541493371660.2165273381013135X-RAY DIFFRACTION99.7582351163
1.8497-1.88990.2106020036371650.2154500477313148X-RAY DIFFRACTION99.699067108
1.8899-1.93380.245569651451690.1953799727033155X-RAY DIFFRACTION99.700059988
1.9338-1.98220.1761390004731660.1983437720943154X-RAY DIFFRACTION99.6697688382
1.9822-2.03580.2242222979311640.1989162055973142X-RAY DIFFRACTION99.5483288166
2.0358-2.09570.2354714635861670.1925948283143148X-RAY DIFFRACTION99.5495495495
2.0957-2.16330.2317314565181640.1946074609783098X-RAY DIFFRACTION99.4209082597
2.1633-2.24070.2014930387851650.1982796801443160X-RAY DIFFRACTION99.4615614717
2.2407-2.33040.1730259931271640.1878327452533103X-RAY DIFFRACTION98.7307343608
2.3304-2.43640.1886664791421660.19465994163128X-RAY DIFFRACTION99.1571342565
2.4364-2.56490.2067267401121630.1944931335743095X-RAY DIFFRACTION98.4587488667
2.5649-2.72560.2687171136451590.1964616719753121X-RAY DIFFRACTION98.2330038934
2.7256-2.9360.2279683249491630.2077282852773079X-RAY DIFFRACTION97.8569272563
2.936-3.23140.2182050603881640.209619209223080X-RAY DIFFRACTION97.8287092883
3.2314-3.69880.1981232425061600.1920535714813065X-RAY DIFFRACTION97.0216606498
3.6988-4.65960.2008122109861600.1677551613533024X-RAY DIFFRACTION95.7593984962
4.6596-49.210.2014830234891540.1982180551412920X-RAY DIFFRACTION92.2845992195

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