[English] 日本語
Yorodumi
- PDB-5jgz: Spin-Labeled T4 Lysozyme Construct T151V1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5jgz
TitleSpin-Labeled T4 Lysozyme Construct T151V1
ComponentsEndolysin
KeywordsHYDROLASE / Spin label / EPR / DEER
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 / Phage lysozyme / Lysozyme domain superfamily / Lysozyme-like domain superfamily
Similarity search - Domain/homology
HEXANE-1,6-DIOL / : / PHOSPHATE ION / Chem-V1A / Endolysin
Similarity search - Component
Biological speciesEnterobacteria phage T4 sensu lato (virus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.534 Å
AuthorsBalo, A.R. / Feyrer, H. / Ernst, O.P.
Funding support Canada, 2items
OrganizationGrant numberCountry
Canada Excellence Research Chairs Program Canada
Natural Sciences and Engineering Research Council (NSERC, Canada) Canada
CitationJournal: Biochemistry / Year: 2016
Title: Toward Precise Interpretation of DEER-Based Distance Distributions: Insights from Structural Characterization of V1 Spin-Labeled Side Chains.
Authors: Balo, A.R. / Feyrer, H. / Ernst, O.P.
History
DepositionApr 20, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 25, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 1.3Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id
Revision 1.5May 1, 2024Group: Advisory / Derived calculations
Category: pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_conn_type
Item: _struct_conn.conn_type_id / _struct_conn.id ..._struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn_type.id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Endolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2887
Polymers18,6301
Non-polymers6576
Water4,756264
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1060 Å2
ΔGint-8 kcal/mol
Surface area8750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.460, 59.460, 95.302
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

-
Components

-
Protein , 1 types, 1 molecules A

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


Mass: 18630.402 Da / Num. of mol.: 1 / Mutation: C54T, C97A, T151C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 sensu lato (virus)
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P00720, lysozyme

-
Non-polymers , 6 types, 270 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-V1A / S-(1-oxyl-2,2,5,5-tetramethyl-2,5-dihydro-1H-imidazol-4-yl) methanesulfonothioate


Mass: 251.346 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15N2O3S2
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Chemical ChemComp-HEZ / HEXANE-1,6-DIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 264 / 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: 2.61 Å3/Da / Density % sol: 52.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: sodium/potassium phosphate, sodium chloride, hexane-1,6-diol, 2-propanol

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU / Detector: CCD / Date: Aug 11, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.534→34.98 Å / Num. obs: 29805 / % possible obs: 100 % / Redundancy: 2 % / Net I/σ(I): 11.46
Reflection shellHighest resolution: 1.534 Å

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1C6T

1c6t


Resolution: 1.534→29.73 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.31
RfactorNum. reflection% reflection
Rfree0.1954 2003 6.72 %
Rwork0.1673 --
obs0.1693 29804 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.534→29.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1299 0 34 264 1597
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061377
X-RAY DIFFRACTIONf_angle_d0.7411858
X-RAY DIFFRACTIONf_dihedral_angle_d9.441857
X-RAY DIFFRACTIONf_chiral_restr0.045204
X-RAY DIFFRACTIONf_plane_restr0.005233
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5341-1.57250.34791390.31211927X-RAY DIFFRACTION99
1.5725-1.6150.25461370.23661958X-RAY DIFFRACTION100
1.615-1.66250.20821410.19141964X-RAY DIFFRACTION100
1.6625-1.71620.20471410.17051961X-RAY DIFFRACTION100
1.7162-1.77750.18631430.16751960X-RAY DIFFRACTION100
1.7775-1.84870.20991380.16561964X-RAY DIFFRACTION100
1.8487-1.93280.20211410.17321962X-RAY DIFFRACTION100
1.9328-2.03470.19941410.15321971X-RAY DIFFRACTION100
2.0347-2.16220.19031450.15051983X-RAY DIFFRACTION100
2.1622-2.32910.21071430.14951980X-RAY DIFFRACTION100
2.3291-2.56340.20331470.16371993X-RAY DIFFRACTION100
2.5634-2.93410.17351430.16632020X-RAY DIFFRACTION100
2.9341-3.69610.16491490.15332026X-RAY DIFFRACTION100
3.6961-29.730.1911550.16882132X-RAY DIFFRACTION100

+
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