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- PDB-5o29: Lytic transglycosylase in action -

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Basic information

Entry
Database: PDB / ID: 5o29
TitleLytic transglycosylase in action
ComponentsTransglycosylase
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 / Soluble lytic murein transglycosylase L domain / Lytic transglycosylase, superhelical U-shaped / Lytic transglycosylase, superhelical linker domain superfamily / Transglycosylase SLT domain 1 / Transglycosylase SLT domain / Lysozyme-like domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
: / Soluble lytic murein transglycosylase
Similarity search - Component
Biological speciesNeisseria meningitidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3785 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
DepositionMay 19, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 14, 2018Provider: repository / Type: Initial release
Revision 1.1May 2, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Nov 28, 2018Group: Data collection / Structure summary / Category: audit_author
Revision 1.3Jan 17, 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
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transglycosylase


Theoretical massNumber of molelcules
Total (without water)65,6851
Polymers65,6851
Non-polymers00
Water15,277848
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area24900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.218, 72.749, 125.225
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 Transglycosylase


Mass: 65684.609 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis (bacteria) / Gene: slt, ERS514729_01258 / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): gold
References: UniProt: A0A0Y5YPU4, UniProt: Q9JXP1*PLUS, Lyases; Carbon-oxygen lyases; Acting on polysaccharides
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 848 / Source method: isolated from a natural source / Formula: H2O
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: 2.33 Å3/Da / Density % sol: 47.23 % / Description: Rod Shape
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 33% (w/v) PEG 6000, Hepes pH 7.5 or 3) 0.2M Zinc acetate, or 0.1 M Sodium cacodylate pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.3785→45.93 Å / Num. obs: 119443 / % possible obs: 93.76 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.1431 / Rpim(I) all: 0.06957 / Net I/σ(I): 10.73
Reflection shellResolution: 1.379→1.428 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 0.4 / Num. unique obs: 11548 / Rpim(I) all: 0.1 / % possible all: 92.1

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YIM

4yim
PDB Unreleased entry


Resolution: 1.3785→45.93 Å / SU ML: 0.17 / Cross valid method: NONE / σ(F): 1.33 / Phase error: 22.79
RfactorNum. reflection% reflection
Rfree0.213 1987 1.67 %
Rwork0.1831 --
obs0.1836 118923 93.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.3785→45.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4479 0 0 848 5327
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054610
X-RAY DIFFRACTIONf_angle_d0.7686248
X-RAY DIFFRACTIONf_dihedral_angle_d4.1952747
X-RAY DIFFRACTIONf_chiral_restr0.072662
X-RAY DIFFRACTIONf_plane_restr0.005834
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3785-1.4130.36221327912X-RAY DIFFRACTION90
1.413-1.45120.31861400.3068465X-RAY DIFFRACTION96
1.4512-1.49390.3061520.28148516X-RAY DIFFRACTION96
1.4939-1.54220.27251570.24728514X-RAY DIFFRACTION97
1.5422-1.59730.25561290.22178566X-RAY DIFFRACTION97
1.5973-1.66120.23221540.2068492X-RAY DIFFRACTION96
1.6612-1.73680.21481330.19488507X-RAY DIFFRACTION96
1.7368-1.82840.19011490.19128427X-RAY DIFFRACTION95
1.8284-1.9430.23381410.20398420X-RAY DIFFRACTION95
1.943-2.0930.2171490.17758399X-RAY DIFFRACTION94
2.093-2.30360.21571410.17468251X-RAY DIFFRACTION92
2.3036-2.63690.1941410.17258278X-RAY DIFFRACTION92
2.6369-3.32210.21691360.17548137X-RAY DIFFRACTION90
3.3221-45.930.17211330.14728052X-RAY DIFFRACTION86

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