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- PDB-5mpq: Bulgecin A: The key to a broad-spectrum inhibitor that targets ly... -

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Basic information

Entry
Database: PDB / ID: 5mpq
TitleBulgecin A: The key to a broad-spectrum inhibitor that targets lytic transglycosylases
ComponentsTransglycosylase
KeywordsLYASE / bulgecin A / LtgA / Lytic Transglycosylase / Peptidoglycan
Function / homology
Function and homology information


catalytic activity / hydrolase activity, hydrolyzing O-glycosyl compounds / periplasmic space / metal ion binding
Similarity search - Function
Lytic transglycosylase, superhelical linker domain superfamily / Lytic transglycosylase, superhelical U-shaped / Transglycosylase SLT domain 1 / Transglycosylase SLT domain / Prokaryotic membrane lipoprotein lipid attachment site profile. / Lysozyme-like domain superfamily
Similarity search - Domain/homology
Chem-BLG / : / Soluble lytic murein transglycosylase
Similarity search - Component
Biological speciesNeisseria meningitidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.78 Å
AuthorsWilliams, A.H.
Funding support France, 1items
OrganizationGrant numberCountry
European Research Council202283 France
CitationJournal: Antibiotics / Year: 2017
Title: Bulgecin A: The Key to a Broad-Spectrum Inhibitor That Targets Lytic Transglycosylases.
Authors: Williams, A.H. / Wheeler, R. / Thiriau, C. / Haouz, A. / Taha, M.K. / Boneca, I.G.
History
DepositionDec 17, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 29, 2017Provider: repository / Type: Initial release
Revision 1.1May 10, 2017Group: Database references
Revision 1.2May 17, 2017Group: Database references
Revision 1.3Jan 17, 2024Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_audit_support / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transglycosylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,5355
Polymers63,7271
Non-polymers8084
Water6,882382
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1390 Å2
ΔGint-4 kcal/mol
Surface area24560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.834, 71.561, 121.123
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Transglycosylase


Mass: 63726.551 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: LtgA, Neisseria Meningitidis / Source: (gene. exp.) Neisseria meningitidis (bacteria) / Gene: slt, ERS514729_01258 / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: A0A0Y5YPU4, UniProt: Q9JXP1*PLUS, Lyases; Carbon-oxygen lyases; Acting on polysaccharides
#2: Chemical ChemComp-BLG / 4-O-(4-O-SULFONYL-N-ACETYLGLUCOSAMININYL)-5-METHYLHYDROXY-L-PROLINE-TAURINE / BULGECIN A


Mass: 552.551 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H30N3O14S2
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-NHE / 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID / N-CYCLOHEXYLTAURINE / CHES


Mass: 207.290 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H17NO3S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 382 / Source method: isolated from a natural source / Formula: H2O

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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: 2.19 Å3/Da / Density % sol: 43.99 % / Description: Long Rod Shape
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.5-2.0 M Ammonium sulfate, 0.1 MES buffer pH 6.5 or 1.5-2.0 M Ammonium sulfate, 0.1 M 2% (v/v) PEG 400 0.1 M Hepes pH. 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.78→45.84 Å / Num. obs: 54379 / % possible obs: 98 % / Redundancy: 2 % / Net I/σ(I): 4.46
Reflection shellHighest resolution: 1.78 Å

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata scaling
REFMACrefinement
PDB_EXTRACT3.22data extraction
PHASERphasing
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YIM

4yim
PDB Unreleased entry


Resolution: 1.78→45.84 Å / Cross valid method: FREE R-VALUE /
Num. reflection% reflection
obs54379 84 %
Displacement parametersBiso max: 70.74 Å2 / Biso mean: 27.3729 Å2 / Biso min: 9.46 Å2
Refinement stepCycle: LAST / Resolution: 1.78→45.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4479 0 49 382 4910

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