[English] 日本語
Yorodumi
- PDB-1p56: Duplication-extension of Helix A of T4 lysozyme -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1p56
TitleDuplication-extension of Helix A of T4 lysozyme
ComponentsPROTEIN (Lysozyme)
KeywordsHYDROLASE / sequence duplication / folding propensity / completion folding experiment
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
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSagermann, M. / Gay, L. / Baase, W.A. / Matthews, B.W.
Citation
Journal: Biochemistry / Year: 2004
Title: Relocation or duplication of the helix A sequence of T4 lysozyme causes only modest changes in structure but can increase or decrease the rate of folding.
Authors: Sagermann, M. / Baase, W.A. / Mooers, B.H. / Gay, L. / Matthews, B.W.
#1: Journal: J.Mol.Biol. / Year: 2002
Title: Crystal structures of a T4-lysozyme duplication-extension mutant demonstrates that the highly conserved beta-sheet region has low intrinsic folding propensity
Authors: Sagermann, M. / 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.
#3: Journal: Proc.Natl.Acad.Sci.USA / Year: 1999
Title: Structural characterization of an engineered tandem repeat contrasts the importance of context and sequence in protein folding
Authors: Sagermann, M. / Baase, W.A. / Matthews, B.W.
History
DepositionApr 25, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Aug 14, 2019Group: Data collection / Category: computing
Revision 1.5Oct 27, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.6Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Remark 999SEQUENCE Residue Leu 164 was deleted and sequence SGGAMNIFEMLRIDE was appended to the C-terminus

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PROTEIN (Lysozyme)


Theoretical massNumber of molelcules
Total (without water)19,9541
Polymers19,9541
Non-polymers00
Water2,162120
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.300, 60.300, 96.396
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

-
Components

#1: Protein PROTEIN (Lysozyme) / Lysis protein / Muramidase / Endolysin


Mass: 19953.857 Da / Num. of mol.: 1 / Mutation: C54T, C97A
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 product E / Plasmid: phs1403 / Production host: Escherichia coli (E. coli) / Strain (production host): RR1 / References: UniProt: P00720, lysozyme
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / 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: 2.75 Å3/Da / Density % sol: 55.25 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 35% PEG 4000, 50mM phosphate buffer, 5% isopropanol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 170 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.999 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 10, 2002 / Details: mirrors
RadiationMonochromator: Flat mirror, single SI crystal bend / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999 Å / Relative weight: 1
ReflectionResolution: 1.7→28.75 Å / Num. obs: 22444 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 14.24 Å2 / Rsym value: 0.066 / Net I/σ(I): 7.2
Reflection shellResolution: 1.79→1.9 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 5.1 / Num. unique all: 3053 / Rsym value: 0.11 / % possible all: 98.7

-
Processing

Software
NameClassification
TNTrefinement
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2LZM

2lzm


Resolution: 1.8→30 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: Only disconnected density could be seen in the vicinity of the old c-terminus. Therefore, the sequence of the appended residues SGGAMNIFEMLRIDE could not be placed reliably into the density ...Details: Only disconnected density could be seen in the vicinity of the old c-terminus. Therefore, the sequence of the appended residues SGGAMNIFEMLRIDE could not be placed reliably into the density and was omitted in the final model.
RfactorNum. reflectionSelection details
Rfree0.273 1926 random
Rwork0.208 --
all0.215 19144 -
obs0.214 17218 -
Displacement parametersBiso mean: 0.74 Å2
Baniso -1Baniso -2Baniso -3
1-0.74 Å20.68 Å20 Å2
2--0.74 Å20 Å2
3----1.48 Å2
Refinement stepCycle: LAST / Resolution: 1.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1292 0 0 120 1412
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.014
X-RAY DIFFRACTIONt_dihedral_angle_d1.777
X-RAY DIFFRACTIONt_angle_deg13.607

+
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