[English] 日本語
Yorodumi
- PDB-212l: PROTEIN STRUCTURE PLASTICITY EXEMPLIFIED BY INSERTION AND DELETIO... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 212l
TitlePROTEIN STRUCTURE PLASTICITY EXEMPLIFIED BY INSERTION AND DELETION MUTANTS IN T4 LYSOZYME
ComponentsT4 LYSOZYME
KeywordsHYDROLASE (O-GLYCOSYL) / GLYCOSIDASE / BACTERIOLYTIC ENZYME
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
2-HYDROXYETHYL DISULFIDE / Endolysin
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / Resolution: 1.76 Å
AuthorsVetter, I.R. / Baase, W.A. / Heinz, D.W. / Xiong, J.-P. / Snow, S. / Matthews, B.W.
Citation
Journal: Protein Sci. / Year: 1996
Title: Protein structural plasticity exemplified by insertion and deletion mutants in T4 lysozyme.
Authors: Vetter, I.R. / Baase, W.A. / Heinz, D.W. / Xiong, J.P. / Snow, S. / Matthews, B.W.
#1: Journal: Nature / Year: 1993
Title: How Amino-Acid Insertions are Allowed in an Alpha-Helix of T4 Lysozyme
Authors: Heinz, D.W. / Baase, W.A. / Dahlquist, F.W. / Matthews, B.W.
#2: Journal: J.Mol.Biol. / Year: 1987
Title: Structure of Bacteriophage T4 Lysozyme Refined at 1.7 A Resolution
Authors: Weaver, L.H. / Matthews, B.W.
History
DepositionSep 23, 1996Processing site: BNL
Revision 1.0Dec 23, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: T4 LYSOZYME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,0672
Polymers18,9131
Non-polymers1541
Water2,792155
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.910, 60.910, 96.730
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

-
Components

#1: Protein T4 LYSOZYME


Mass: 18912.678 Da / Num. of mol.: 1 / Mutation: C54T, C97A, INS(L164-AAAA)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 (virus) / Genus: T4-like viruses / Species: Enterobacteria phage T4 sensu lato / Gene: T4 LYSOZYME GENE / Plasmid: M13 / Gene (production host): T4 LYSOZYME GENE / Production host: Escherichia coli (E. coli) / References: UniProt: P00720, lysozyme
#2: Chemical ChemComp-HED / 2-HYDROXYETHYL DISULFIDE


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 155 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.83 Å3/Da / Density % sol: 48.3 %
Crystal growDetails: MUTANT CRYSTALLIZED FROM PEG IN CONTRAST TO L164AAAA WHICH WAS CRYSTALLIZED FROM PHOSPHATE.
Crystal
*PLUS
Crystal grow
*PLUS
pH: 7.5 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
118 %PEG800011
20.1 MHEPES11
350 mMbeta-mercaptoethanol11

-
Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR / Date: Nov 2, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.76→35.65 Å / Num. obs: 20392 / % possible obs: 95.3 % / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Rmerge(I) obs: 0.0622

-
Processing

Software
NameClassification
TNTrefinement
UCSDdata reduction
RefinementResolution: 1.76→35.65 Å / σ(F): 0
Details: RESIDUES 162 - 168 IN THIS MUTANT LYSOZYME ARE EXTREMELY MOBILE. THUS THE COORDINATES FOR THESE RESIDUES ARE VERY UNRELIABLE. THIS MUTANT WAS CRYSTALLIZED FROM PEG, AS COMPARED TO ENTRY 219L ...Details: RESIDUES 162 - 168 IN THIS MUTANT LYSOZYME ARE EXTREMELY MOBILE. THUS THE COORDINATES FOR THESE RESIDUES ARE VERY UNRELIABLE. THIS MUTANT WAS CRYSTALLIZED FROM PEG, AS COMPARED TO ENTRY 219L WHICH IS THE SAME MUTANT, BUT CRYSTALLIZED FROM PHOSPHATE.
RfactorNum. reflection% reflection
Rwork0.156 --
all-20392 -
obs-20392 95.3 %
Refinement stepCycle: LAST / Resolution: 1.76→35.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1328 0 8 155 1491
Refine LS restraints
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_bond_d0.0130.8
X-RAY DIFFRACTIONt_angle_deg21.5
X-RAY DIFFRACTIONt_dihedral_angle_d15.10
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes0.0193
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.156
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: t_plane_restr / Dev ideal: 0.019 / Weight: 3

+
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