[English] 日本語
Yorodumi
- PDB-260l: AN ADAPTABLE METAL-BINDING SITE ENGINEERED INTO T4 LYSOZYME -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 260l
TitleAN ADAPTABLE METAL-BINDING SITE ENGINEERED INTO T4 LYSOZYME
ComponentsPROTEIN (LYSOZYME)
KeywordsHYDROLASE / HYDROLASE (O-GLYCOSYL) / T4 LYSOZYME / METAL BINDING / PROTEIN ENGINEERING / PROTEIN DESIGN
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 / Lysozyme domain superfamily / Phage lysozyme / Lysozyme / Lysozyme-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
NICKEL (II) ION / Endolysin
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsWray, J.W. / Baase, W.A. / Ostheimer, G.J. / Matthews, B.W.
Citation
Journal: Protein Eng. / Year: 2000
Title: Use of a non-rigid region in T4 lysozyme to design an adaptable metal-binding site.
Authors: Wray, J.W. / Baase, W.A. / Ostheimer, G.J. / Zhang, X.J. / Matthews, B.W.
#1: Journal: Protein Sci. / Year: 1992
Title: Structure of a Stabilizing Disulfide Bridge Mutant that Closes the Active Site Cleft of T4 Lysozyme
Authors: Jacobson, R. / Matsumura, M. / Faber, H.R. / Matthews, B.W.
#2: Journal: Science / Year: 1989
Title: Control of Enzyme Activity by an Engineered Disulfide Bond
Authors: Matsumura, M. / Matthews, B.W.
#3: Journal: J.Mol.Biol. / Year: 1987
Title: Structure of Bacteriophage T4 Lysozyme Refined at 1.7 Angstrom Resolution
Authors: Weaver, L.H. / Matthews, B.W.
History
DepositionMar 1, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Sep 11, 2000Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / 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 / _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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PROTEIN (LYSOZYME)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8915
Polymers18,7021
Non-polymers1884
Water1,928107
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.170, 62.170, 96.780
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Cell settingtrigonal
Space group name H-MP3221

-
Components

#1: Protein PROTEIN (LYSOZYME) / E.C.3.2.1.17


Mass: 18702.449 Da / Num. of mol.: 1 / Mutation: C54T,C97A,T21H,T142H
Source method: isolated from a genetically manipulated source
Details: T4 LYSOZYME MUTANT WITH CYS 54 REPLACED BY THR, CYS 97 REPLACED BY ALA, THR 21 REPLACED BY HIS, THR 142 REPLACED BY HIS
Source: (gene. exp.) Enterobacteria phage T4 (virus) / Genus: T4-like viruses / Species: Enterobacteria phage T4 sensu lato
Description: BACTERIOPHAGE T4 (MUTANT GENE DERIVED FROM THE M13 PLASMID BY CLONING THE T4 LYSOZYME GENE)
Cellular location: CYTOPLASM / Gene: GENE E FROM BACTERIOPHAGE T4 / Plasmid: PHS1403 / Gene (production host): T4 LYSOZYME / Production host: Escherichia coli (E. coli) / Strain (production host): RR1 / 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-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 107 / Source method: isolated from a natural source / Formula: H2O
Compound detailsSTRUCTURE OF A T4 LYSOZYME MUTANT WITH AN ENGINEERED METAL BINDING SITE. THIS MUTANT DESIGNATED ...STRUCTURE OF A T4 LYSOZYME MUTANT WITH AN ENGINEERED METAL BINDING SITE. THIS MUTANT DESIGNATED H2NI IS THE PROTEIN WHICH CONTAINS THE METAL BINDING SITE WITH NI +2 BOUND. THE METAL LIGANDS CO, AND ZN WILL BE DESCRIBED AS SEPARATE PDB FILES AND INCLUDED IN THE PAPER "AN ADAPTABLE METAL BINDING SITE ENGINEERED INTO T4 LYSOZYME.
Nonpolymer detailsNICKEL 2+ IS BOUND TO THE ENGINEERED PROTEIN LIGANDS HIS 21 AND HIS 142, WITH HOH 501-504 AS THE ...NICKEL 2+ IS BOUND TO THE ENGINEERED PROTEIN LIGANDS HIS 21 AND HIS 142, WITH HOH 501-504 AS THE REMAINING LIGANDS. A SECOND NI SITE IS FORMED FROM THE NITROGEN OF MET 1, HOH 601-603, AND OXYGEN FROM GLU 64 IN A SYMMETRY-RELATED MOLECULE
Sequence detailsRESIDUES 163 AND 164 ARE DISORDERED AND NOT OBSERVABLE IN ELECTRON DENSITY MAPS. THEREFORE THEY ARE ...RESIDUES 163 AND 164 ARE DISORDERED AND NOT OBSERVABLE IN ELECTRON DENSITY MAPS. THEREFORE THEY ARE ABSENT FROM THE COORDINATE FILE.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.82 Å3/Da / Density % sol: 56.43 % / Description: STARTING MODEL WAS CYS-FREE WILDTYPE LYSOZYME
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Components of the solutions
IDNameCrystal-IDSol-ID
1HEPES11
2NACLSodium chloride11
3ISOPROPANOL11
4PEG 800011
5NICL211
6HEPES12
7NACLSodium chloride12
8ISOPROPANOL12
9PEG 800012
10NICL212
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
1200-300 mM1reservoirNaCl
220 mMHEPES1reservoir
312-16 %PEG80001reservoir
410 %2-propanol1reservoir
52 mMmetal ion1reservoiras the chloride or acetate salt
61 mMprotein1drop
720 mMHEPES1drop
81
91
101

-
Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: SDMS / Detector: AREA DETECTOR / Date: Jan 19, 1998 / Details: GRAPHITE MONOCHROMATOR
RadiationMonochromator: NI FILTER/GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. obs: 19963 / % possible obs: 92 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.031
Reflection shellHighest resolution: 1.8 Å / Rmerge(I) obs: 0.18 / Mean I/σ(I) obs: 2

-
Processing

Software
NameVersionClassification
TNTrefinement
SDMSDETECTOR SYSTEM (NIELSEN)data reduction
SDMSDETECTOR SYSTEM (NIELSEN)data scaling
TNTphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→20 Å / σ(F): 0 / Stereochemistry target values: TNT PROTGEO / Details: STARTING MODEL WAS CYS-FREE WILDTYPE
RfactorNum. reflection% reflection
Rwork0.19 --
all-19963 -
obs-19963 92 %
Solvent computationSolvent model: BABENET SCALING / Bsol: 790 Å2 / ksol: 1 e/Å3
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1298 0 4 107 1409
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.016
X-RAY DIFFRACTIONt_angle_deg2.16
X-RAY DIFFRACTIONt_dihedral_angle_d0
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.01
X-RAY DIFFRACTIONt_gen_planes0.015
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd0.08
Software
*PLUS
Name: TNT / Version: 5F / Classification: refinement
Refinement
*PLUS
σ(F): 0 / Rfactor all: 0.19
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_angle_deg2.16
X-RAY DIFFRACTIONt_dihedral_angle_d0
X-RAY DIFFRACTIONt_planar_d0.01
X-RAY DIFFRACTIONt_plane_restr0.015

+
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