[English] 日本語
Yorodumi
- PDB-1c6n: T4 LYSOZYME MUTANT C54T/C97A/L99A/F153A IN THE PRESENCE OF 8 ATM XENON -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1c6n
TitleT4 LYSOZYME MUTANT C54T/C97A/L99A/F153A IN THE PRESENCE OF 8 ATM XENON
ComponentsPROTEIN (LYSOZYME)
KeywordsHYDROLASE / HYDROLASE (O-GLYCOSYL) / T4 LYSOZYME / NOBLE GAS BINDING
Function / homology
Function and homology information


viral release from host cell by cytolysis / peptidoglycan catabolic process / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to bacterium / host cell cytoplasm
Similarity search - Function
Lysozyme - #40 / Endolysin T4 type / T4-type lysozyme / Glycoside hydrolase, family 24 / Lysozyme domain superfamily / Phage lysozyme / Lysozyme / Lysozyme-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / XENON / Endolysin
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsQuillin, M.L. / Matthews, B.W.
Citation
Journal: J.Mol.Biol. / Year: 2000
Title: Size versus polarizability in protein-ligand interactions: binding of noble gases within engineered cavities in phage T4 lysozyme.
Authors: Quillin, M.L. / Breyer, W.A. / Griswold, I.J. / Matthews, B.W.
#1: Journal: Science / Year: 1992
Title: Response of a Protein Structure to Cavity-Creating Mutations and its Relation to the Hydrophobic Effect
Authors: Eriksson, A.E. / Baase, W.A. / Zhang, X.-J. / Heinz, D.W. / Blaber, M. / Baldwin, E.P. / 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
DepositionDec 21, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Oct 4, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PROTEIN (LYSOZYME)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2639
Polymers18,5101
Non-polymers7528
Water1,802100
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.166, 61.166, 97.068
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

-
Components

#1: Protein PROTEIN (LYSOZYME)


Mass: 18510.188 Da / Num. of mol.: 1 / Mutation: YES
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: GENE E / Plasmid: PHS1403 / Production host: Escherichia coli (E. coli) / References: UniProt: P00720, lysozyme
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-XE / XENON / Xenon


Mass: 131.293 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Xe
#4: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL / 2-Mercaptoethanol


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 100 / 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: 2.8 Å3/Da / Density % sol: 56 %
Crystal growDetails: 1.8-2.2 M NAH2/K2HPO4, PH 6.9-7.1, 50 MM BETA-MERCAPTOETHANOL AND/OR 50 MM HYDROXYETHYL DISULFIDE
PH range: 6.9-7
Crystal grow
*PLUS
pH: 6.7 / Method: batch method / Details: Remington, S.J., (1978) J.Mol.Biol., 118, 81.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mg/mlprotein11
20.55 M11NaCl
314 mMmercaptoethanol11
41 mM11MgCl2
50.01 Msodium phosphate11
62.2 M11NaH2PO4
71.8 M11K2HPO4

-
Data collection

DiffractionMean temperature: 273 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Feb 2, 1999
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→60 Å / Num. obs: 9626 / % possible obs: 86.2 % / Observed criterion σ(I): 0 / Redundancy: 2.41 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 8.3
Reflection shellResolution: 2.2→2.24 Å / Rmerge(I) obs: 0.26 / % possible all: 59.4
Reflection
*PLUS
% possible obs: 83 %
Reflection shell
*PLUS
% possible obs: 59.4 %

-
Processing

Software
NameClassification
TNTrefinement
DENZOdata reduction
SCALEPACKdata scaling
TNTphasing
RefinementStarting model: 1L89
Resolution: 2.2→60 Å / Isotropic thermal model: TNT BCORREL / σ(F): 0 / Stereochemistry target values: TNT PROTGEO
RfactorNum. reflection% reflection
all0.186 9624 -
obs-9624 86.2 %
Solvent computationSolvent model: MOEWS AND KRETSINGER / Bsol: 314.6 Å2 / ksol: 0.95 e/Å3
Refinement stepCycle: LAST / Resolution: 2.2→60 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1283 0 14 100 1397
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.0213090.8
X-RAY DIFFRACTIONt_angle_deg2.97917571.3
X-RAY DIFFRACTIONt_dihedral_angle_d16.278000
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.012342
X-RAY DIFFRACTIONt_gen_planes0.0161885
X-RAY DIFFRACTIONt_it4.57213091
X-RAY DIFFRACTIONt_nbd0.042510
Software
*PLUS
Name: TNT / Version: 5E / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg16.270
X-RAY DIFFRACTIONt_plane_restr0.0165

+
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