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- PDB-5vnq: Neutron crystallographic structure of perdeuterated T4 lysozyme c... -

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Basic information

Entry
Database: PDB / ID: 5vnq
TitleNeutron crystallographic structure of perdeuterated T4 lysozyme cysteine-free pseudo-wild type at cryogenic temperature
ComponentsEndolysin
KeywordsHYDROLASE / T4 lysozyme / Neutron Crystallography / Hydrogen bonding network / Hydrogen bond / Water
Function / homology
Function and homology information


viral release from host cell by cytolysis / peptidoglycan catabolic process / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / host cell cytoplasm / defense response to bacterium
Similarity search - Function
Lysozyme - #40 / Endolysin T4 type / T4-type lysozyme / : / Glycoside hydrolase, family 24 / Phage lysozyme / Lysozyme domain superfamily / Lysozyme / Lysozyme-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DEUTERATED WATER / Endolysin / Endolysin
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
MethodNEUTRON DIFFRACTION / NUCLEAR REACTOR / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsLi, L. / Shukla, S. / Meilleur, F. / Standaert, R.F. / Pierce, J. / Myles, D.A.A. / Cuneo, M.J.
CitationJournal: Protein Sci. / Year: 2017
Title: Neutron crystallographic studies of T4 lysozyme at cryogenic temperature.
Authors: Li, L. / Shukla, S. / Meilleur, F. / Standaert, R.F. / Pierce, J. / Myles, D.A.A. / Cuneo, M.J.
History
DepositionMay 1, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 26, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Sep 9, 2020Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Endolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6993
Polymers18,6281
Non-polymers712
Water64936
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.500, 61.500, 95.900
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Endolysin / Lysis protein / Lysozyme / Muramidase


Mass: 18628.363 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 (virus) / Gene: e, T4Tp126 / Production host: Escherichia coli (E. coli) / References: UniProt: D9IEF7, UniProt: P00720*PLUS, lysozyme
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-DOD / water


Mass: 18.015 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Formula: D2O

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Experimental details

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Experiment

ExperimentMethod: NEUTRON DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: ~2.0 M Na/K phosphate, pH 6-7, 250 mM NaCl, 40mM 2-hydroxyethyl disulfide
PH range: 6-7

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: NUCLEAR REACTOR / Site: ORNL High Flux Isotope Reactor / Beamline: CG4D / Wavelength: 2.8 - 4.6
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Oct 4, 2016
RadiationProtocol: LAUE / Monochromatic (M) / Laue (L): L / Scattering type: neutron
Radiation wavelength
IDWavelength (Å)Relative weight
12.81
24.61
ReflectionResolution: 2.2→16.7 Å / Num. obs: 7965 / % possible obs: 72.7 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.162 / Net I/σ(I): 6.5
Reflection shellResolution: 2.2→2.32 Å / Rmerge(I) obs: 0.214

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Processing

SoftwareName: PHENIX / Version: (1.11.1_2575: ???) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LW9

1lw9


Resolution: 2.2→16.7 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.43 / Phase error: 18.63
RfactorNum. reflection% reflection
Rfree0.2802 190 2.39 %
Rwork0.2421 --
obs0.2431 7964 70.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refine LS restraints
Refine-IDTypeDev idealNumber
NEUTRON DIFFRACTIONf_bond_d0.0043066
NEUTRON DIFFRACTIONf_angle_d0.6585440
NEUTRON DIFFRACTIONf_dihedral_angle_d19.306842
NEUTRON DIFFRACTIONf_chiral_restr0.035200
NEUTRON DIFFRACTIONf_plane_restr0.002601
LS refinement shellResolution: 2.1829→16.6495 Å
RfactorNum. reflection% reflection
Rfree0.2802 190 -
Rwork0.2421 7774 -
obs--70 %

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