[English] 日本語
Yorodumi
- PDB-6l00: Crystal structure of the cell-wall binding domain (CBD) of endoly... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6l00
TitleCrystal structure of the cell-wall binding domain (CBD) of endolysin LysIME-EF1
ComponentsLysin
KeywordsLYASE
Function / homologyCHAP domain profile. / CHAP domain / CHAP domain / Papain-like cysteine peptidase superfamily / Lysin
Function and homology information
Biological speciesEnterococcus phage IMEEF1 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsOuyang, S.Y. / Zhen, X.K.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China31800159 China
National Natural Science Foundation of China31770948 China
CitationJournal: Plos Pathog. / Year: 2020
Title: Structural and functional insights into a novel two-component endolysin encoded by a single gene in Enterococcus faecalis phage.
Authors: Zhou, B. / Zhen, X. / Zhou, H. / Zhao, F. / Fan, C. / Perculija, V. / Tong, Y. / Mi, Z. / Ouyang, S.
History
DepositionSep 25, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 19, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 15, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 22, 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: Lysin


Theoretical massNumber of molelcules
Total (without water)8,1661
Polymers8,1661
Non-polymers00
Water95553
1
A: Lysin

A: Lysin

A: Lysin

A: Lysin


Theoretical massNumber of molelcules
Total (without water)32,6664
Polymers32,6664
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area5280 Å2
ΔGint-55 kcal/mol
Surface area13390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.880, 59.880, 87.010
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422

-
Components

#1: Protein Lysin /


Mass: 8166.395 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus phage IMEEF1 (virus) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: S5MRN1
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 53 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.39 Å3/Da / Density % sol: 48.49 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 7 / Details: 20% PEG 4000, 0.2 M NaCl

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 20, 2018
RadiationMonochromator: SSRF BEAMLINE BL17U1 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.75→49.33 Å / Num. obs: 8236 / % possible obs: 99 % / Redundancy: 9.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.089 / Rsym value: 0.091 / Net I/σ(I): 2.3
Reflection shellResolution: 1.75→1.813 Å / Num. unique obs: 552 / CC1/2: 0.696
Serial crystallography sample deliveryMethod: fixed target

-
Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.8refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6IST

6ist


Resolution: 1.75→42.342 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 27.75
RfactorNum. reflection% reflection
Rfree0.2438 814 9.89 %
Rwork0.2231 --
obs0.2251 8231 98.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 57.43 Å2 / Biso mean: 27.2266 Å2 / Biso min: 15.95 Å2
Refinement stepCycle: final / Resolution: 1.75→42.342 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms566 0 0 53 619
Biso mean---34.05 -
Num. residues----70

+
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