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- PDB-5o24: Lytic transglycosylase in action -

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Basic information

Entry
Database: PDB / ID: 5o24
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 - #10 / Lysozyme / Lysozyme-like domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. ...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 - #10 / Lysozyme / Lysozyme-like domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
: / Soluble lytic murein transglycosylase
Similarity search - Component
Biological speciesNeisseria meningitidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.429 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 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)65,7254
Polymers65,1031
Non-polymers6223
Water15,259847
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1030 Å2
ΔGint14 kcal/mol
Surface area24910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.714, 72.681, 124.924
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: 65103.008 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)
References: UniProt: A0A0Y5YPU4, UniProt: Q9JXP1*PLUS, Lyases; Carbon-oxygen lyases; Acting on polysaccharides
#2: Chemical ChemComp-NHE / 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID / N-CYCLOHEXYLTAURINE / CHES


Mass: 207.290 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H17NO3S / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 847 / 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: 47.12 % / Description: Rod Shape
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 9.5
Details: 100 mM CHES pH 9.5, 100 mM tri sodium citrate, 30% PEG 3000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.429→45.74 Å / Num. obs: 110571 / % possible obs: 97.46 % / Redundancy: 9.3 % / Rmerge(I) obs: 0.185 / Rpim(I) all: 0.06356 / Net I/σ(I): 14.4
Reflection shellResolution: 1.429→1.48 Å / Redundancy: 8.8 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 0.41 / Num. unique obs: 10064 / Rpim(I) all: 0.8801 / % possible all: 90.47

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YIM

4yim
PDB Unreleased entry


Resolution: 1.429→45.74 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.37
RfactorNum. reflection% reflection
Rfree0.224 2002 1.82 %
Rwork0.1909 --
obs0.1915 110025 97.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.429→45.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4479 0 39 847 5365
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054640
X-RAY DIFFRACTIONf_angle_d0.7716287
X-RAY DIFFRACTIONf_dihedral_angle_d15.3611737
X-RAY DIFFRACTIONf_chiral_restr0.071665
X-RAY DIFFRACTIONf_plane_restr0.005831
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4287-1.46440.37331340.34816799X-RAY DIFFRACTION88
1.4644-1.5040.34671370.31817563X-RAY DIFFRACTION96
1.504-1.54820.33291270.28527620X-RAY DIFFRACTION97
1.5482-1.59820.27541360.26337606X-RAY DIFFRACTION97
1.5982-1.65530.29251510.2427614X-RAY DIFFRACTION97
1.6553-1.72160.27651450.22557707X-RAY DIFFRACTION98
1.7216-1.80.25471510.20887671X-RAY DIFFRACTION98
1.8-1.89490.23961360.20187768X-RAY DIFFRACTION98
1.8949-2.01360.26171450.19577781X-RAY DIFFRACTION98
2.0136-2.16910.21251450.18117786X-RAY DIFFRACTION99
2.1691-2.38740.1961400.17567867X-RAY DIFFRACTION99
2.3874-2.73280.22731510.1877937X-RAY DIFFRACTION99
2.7328-3.44290.20981460.18118001X-RAY DIFFRACTION99
3.4429-49.17730.19141580.16498303X-RAY DIFFRACTION100

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