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- PDB-6fpn: Lytic transglycosylase in action -

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Basic information

Entry
Database: PDB / ID: 6fpn
TitleLytic transglycosylase in action
ComponentsPutative soluble lytic murein transglycosylase
KeywordsHYDROLASE / lytic transglycosylases / acid/base catalysis / peptidoglycan / bacteria
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
Soluble lytic murein transglycosylase
Similarity search - Component
Biological speciesNeisseria meningitidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.44 Å
AuthorsWilliams, A.H. / Hoauz, A. / Boneca, I.G.
CitationJournal: J. Biol. Chem. / Year: 2018
Title: A step-by-stepin crystalloguide to bond cleavage and 1,6-anhydro-sugar product synthesis by a peptidoglycan-degrading lytic transglycosylase.
Authors: Williams, A.H. / Wheeler, R. / Rateau, L. / Malosse, C. / Chamot-Rooke, J. / Haouz, A. / Taha, M.K. / Boneca, I.G.
History
DepositionFeb 11, 2018Deposition site: PDBE / Processing site: PDBE
SupersessionMar 14, 2018ID: 4YIM
Revision 1.0Mar 14, 2018Provider: repository / Type: Initial release
Revision 1.1May 16, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Nov 28, 2018Group: Data collection / Structure summary / Category: audit_author
Revision 1.3May 1, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Putative soluble lytic murein transglycosylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,4418
Polymers64,7691
Non-polymers6727
Water12,989721
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1260 Å2
ΔGint-90 kcal/mol
Surface area26320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.048, 72.966, 124.605
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Putative soluble lytic murein transglycosylase


Mass: 64768.680 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis (bacteria) / Strain: MC58 / Gene: NMB1949 / Plasmid: PGEX-4T1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / Variant (production host): Gold / References: UniProt: Q9JXP1
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 721 / 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: 2.35 Å3/Da / Density % sol: 47.73 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 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: Nov 15, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→62.96 Å / Num. obs: 117919 / % possible obs: 97.42 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 12.16
Reflection shellResolution: 1.4→1.449 Å

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Processing

Software
NameClassification
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 502N

502n


Resolution: 1.44→62.96 Å / Cross valid method: FREE R-VALUE /
Num. reflection% reflection
obs117919 97.42 %
Refinement stepCycle: LAST / Resolution: 1.44→62.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4552 0 35 726 5313

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