[English] 日本語
Yorodumi
- PDB-6u0e: Neutron crystal structure of T4L M6AE -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6u0e
TitleNeutron crystal structure of T4L M6AE
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
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / NEUTRON DIFFRACTION / NUCLEAR REACTOR / MOLECULAR REPLACEMENT / Resolution: 2.106 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 1.0Sep 2, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Endolysin


Theoretical massNumber of molelcules
Total (without water)18,5681
Polymers18,5681
Non-polymers00
Water54030
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.800, 60.800, 97.070
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

-
Components

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


Mass: 18568.244 Da / Num. of mol.: 1 / Mutation: M6A, C54T, C97A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 (virus) / Gene: e, T4Tp126 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: D9IEF7, lysozyme
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

Experiment
MethodNumber of used crystals
X-RAY DIFFRACTION1
NEUTRON DIFFRACTION1

-
Sample preparation

CrystalDensity Matthews: 2.79 Å3/Da / Density % sol: 55.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: ~2.0 M Na/K phosphate, pH 6-7, 250 mM NaCl

-
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 CAMERA2PIXELAug 1, 2017
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2LAUELneutron2
Radiation wavelength
IDWavelength (Å)Relative weight
11.54181
221
341
Reflection

Entry-ID: 6U0E

Resolution (Å)Num. obs% possible obs (%)Redundancy (%)Biso Wilson estimate (Å2)Rmerge(I) obsDiffraction-IDNet I/σ(I)CC1/2Rrim(I) all
2.1-501192195.4231.10.06818.9
1.9-151569391.24.323.30.141629.30.9890.1583
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. unique obsDiffraction-IDCC1/2Rpim(I) allRrim(I) all
2.1-2.180.457211641
1.9-1.9560.25672.62120120.1380.16560.3087

-
Processing

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

Cross valid method: THROUGHOUT / Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Stereochemistry target values: ML / Solvent model: FLAT BULK SOLVENT MODEL

Method to determine structureStarting modelResolution (Å)Refine-IDBiso max (Å2)Biso mean (Å2)Biso min (Å2)Rfactor RfreeRfactor RworkRfactor obsNum. reflection RfreeNum. reflection RworkNum. reflection obs% reflection Rfree (%)% reflection obs (%)SU MLσ(F)Phase error
MOLECULAR REPLACEMENT5vnq

5vnq

2.106-29.011X-RAY DIFFRACTION143.341.201214.790.23540.18390.186458111341119214.8795.480.251.3423.89
1.889-14.505NEUTRON DIFFRACTION0.2540.21660.2184772156934.9291.460
Refinement stepCycle: final / Resolution: 2.106→29.011 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1305 0 0 87 1392
Biso mean---46.8 -
Num. residues----164
LS refinement shell

Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.889-2.0070.33551130.32732075NEUTRON DIFFRACTION78
2.007-2.16150.32031250.28182492NEUTRON DIFFRACTION92
2.1615-2.37820.3311330.25492497NEUTRON DIFFRACTION93
2.3782-2.72040.24271250.24262528NEUTRON DIFFRACTION93
2.7204-3.41990.23191320.23312631NEUTRON DIFFRACTION96
3.4199-14.5050.21921440.16152698NEUTRON DIFFRACTION95
2.106-2.31770.30591380.22222598X-RAY DIFFRACTION90
2.3177-2.65290.24611390.21532839X-RAY DIFFRACTION97
2.6529-3.34160.26521450.20052898X-RAY DIFFRACTION98
3.3416-29.0110.20571590.15893006X-RAY DIFFRACTION97

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more