[English] 日本語
Yorodumi
- PDB-2b7x: Sequential reorganization of beta-sheet topology by insertion of ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2b7x
TitleSequential reorganization of beta-sheet topology by insertion of a single strand
ComponentsLysozyme
KeywordsHYDROLASE / sequence duplication / protein design / structural switches / tandem repeat
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
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsSagermann, M. / Matthews, B.W.
Citation
Journal: Protein Sci. / Year: 2006
Title: Sequential reorganization of beta-sheet topology by insertion of a single strand.
Authors: Sagermann, M. / Baase, W.A. / Matthews, B.W.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2003
Title: Long distance conformation changes in a protein engineered by modulated sequence duplication
Authors: Sagermann, M. / Gay, L. / Mattews, B.W.
#2: 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
DepositionOct 5, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 1, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Lysozyme
B: Lysozyme
C: Lysozyme
D: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,70112
Polymers76,9324
Non-polymers7698
Water0
1
A: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4253
Polymers19,2331
Non-polymers1922
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: Lysozyme


Theoretical massNumber of molelcules
Total (without water)19,2331
Polymers19,2331
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5214
Polymers19,2331
Non-polymers2883
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
D: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5214
Polymers19,2331
Non-polymers2883
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)61.380, 78.080, 143.350
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

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


Mass: 19233.061 Da / Num. of mol.: 4
Mutation: C54T, C97A, residues (YTIGIG) inserted after residue G30
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: E / Plasmid: phs1403 / Production host: Escherichia coli (E. coli) / Strain (production host): rr1 / References: UniProt: P00720, lysozyme
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.23 Å3/Da / Density % sol: 44.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: Polyehtylene glycol 4000, 50mM Ammonium sulfate, , pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 6, 1998 / Details: mirrors
RadiationMonochromator: mirrors on si-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→20 Å / Num. all: 14371 / Num. obs: 10387 / % possible obs: 72.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.065 / Net I/σ(I): 7.4
Reflection shellResolution: 3→3.25 Å / % possible all: 66.5

-
Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3LZM,

3lzm


Resolution: 3→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: data was collected on very fragile, thin crystal plates resulting in low occupancy of reflections in data set. Several (non-isomorphous data sets were collected to further verify ...Details: data was collected on very fragile, thin crystal plates resulting in low occupancy of reflections in data set. Several (non-isomorphous data sets were collected to further verify interpretation. Refinement was carried out with the programs refmac and CNS.the sequence between residues 32 and 44 (new mutant numbering) were deleted from the model due to poor density. The c-terminal residues N169 and L170 (new mutant numbering) could not be identified in the density and were therefore omitted.
RfactorNum. reflectionSelection details
Rfree0.3191 521 random according to CNS
Rwork0.2387 --
all0.241 10387 -
obs0.241 10387 -
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.922 Å20 Å20 Å2
2---0.88 Å20 Å2
3---2.802 Å2
Refinement stepCycle: LAST / Resolution: 3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5045 0 40 0 5085
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_refined_d0.025
X-RAY DIFFRACTIONc_angle_refined_deg2.1

+
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