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- PDB-6u0b: Neutron crystal structure of wtT4LD -

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Basic information

Entry
Database: PDB / ID: 6u0b
TitleNeutron crystal structure of wtT4LD
ComponentsEndolysinLysin
KeywordsHYDROLASE / T4 Lysozyme / cavity
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
Endolysin T4 type / T4-type lysozyme / Glycoside hydrolase, family 24 / Lysozyme domain superfamily / Phage lysozyme / Lysozyme-like domain superfamily
Similarity search - Domain/homology
Endolysin / Endolysin
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / NEUTRON DIFFRACTION / NUCLEAR REACTOR / MOLECULAR REPLACEMENT / Resolution: 1.951 Å
AuthorsCuneo, M.J. / Myles, D.A. / Li, L.
CitationJournal: To be published
Title: Solvent entry into cavities of T4 lysozyme.
Authors: Li, L. / Myles, D.A. / Cuneo, M.J.
History
DepositionAug 14, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Endolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6642
Polymers18,6281
Non-polymers351
Water55831
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.870, 60.870, 97.000
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

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


Mass: 18628.363 Da / Num. of mol.: 1 / Mutation: C54T, C97A
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 / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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Experimental details

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Experiment

Experiment
MethodNumber of used crystals
X-RAY DIFFRACTION1
NEUTRON DIFFRACTION1

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Sample preparation

CrystalDensity Matthews: 2.78 Å3/Da / Density % sol: 55.83 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: ~2.0 M Na/K phosphate, pH 6-7, 250 mM NaCl

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Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
12981N
22981N
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
ROTATING ANODERIGAKU MICROMAX-007 HF11.5418
NUCLEAR REACTORORNL Spallation Neutron Source MANDI22.0-4.0
Detector
TypeIDDetectorDate
RIGAKU RAXIS IV++1IMAGE PLATEAug 1, 2017
ORNL ANGER CAMERA2IMAGE PLATEAug 1, 2017
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1MIRRORSSINGLE WAVELENGTHMx-ray1
2LAUELneutron2
Radiation wavelength
IDWavelength (Å)Relative weight
11.54181
221
341
Reflection

Entry-ID: 6U0B

Resolution (Å)Num. obs% possible obs (%)Redundancy (%)Rmerge(I) obsDiffraction-IDNet I/σ(I)
1.95-351567799.95.80.109116.7
2.1-151007178.83.30.17826.5
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. unique obsDiffraction-ID
1.95-2.020.4624.715351
2.1-2.180.27432.688462

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
Mantiddata reduction
LaueViewdata scaling
PHASERphasing
Refinement

% reflection Rfree: 4.97 % / SU ML: 0.19 / Cross valid method: THROUGHOUT / Method to determine structure: MOLECULAR REPLACEMENT / Phase error: 19.88 / Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Starting model: 5VNQ

5vnq

Resolution (Å)Refine-IDBiso max (Å2)Biso mean (Å2)Biso min (Å2)Rfactor RfreeRfactor RworkRfactor obsNum. reflection RfreeNum. reflection obs% reflection obs (%)Diffraction-IDσ(F)
1.951-35X-RAY DIFFRACTION115.2530.58312.070.19840.16410.16586311567799.9711.35
2.101-14.457NEUTRON DIFFRACTION0.2510.21870.22045011007180.1420
Refinement stepCycle: final / Resolution: 1.951→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1309 0 1 91 1401
Biso mean--28.4 37.82 -
Num. residues----164
LS refinement shell

Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.101-2.31160.29291110.27262125NEUTRON DIFFRACTION73
2.3116-2.64440.24411230.24622437NEUTRON DIFFRACTION82
2.6444-3.32490.25251410.24182501NEUTRON DIFFRACTION85
3.3249-14.4570.23881260.18152507NEUTRON DIFFRACTION81
1.951-2.07280.26481300.19612430X-RAY DIFFRACTION100
2.0728-2.23280.19921250.16332440X-RAY DIFFRACTION100
2.2328-2.45740.22161210.16572447X-RAY DIFFRACTION100
2.4574-2.81290.22051290.18112471X-RAY DIFFRACTION100
2.8129-3.54340.18731380.18432495X-RAY DIFFRACTION100
3.5434-350.18091360.14082616X-RAY DIFFRACTION100

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