[English] 日本語
Yorodumi
- PDB-1jhe: LEXA L89P Q92W E152A K156A MUTANT -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1jhe
TitleLEXA L89P Q92W E152A K156A MUTANT
ComponentsLEXA REPRESSORRepressor lexA
KeywordsHYDROLASE / LexA SOS repressor / C-terminal
Function / homology
Function and homology information


repressor LexA / SOS response / DNA-binding transcription repressor activity / protein-DNA complex / DNA replication / transcription cis-regulatory region binding / serine-type endopeptidase activity / DNA repair / negative regulation of DNA-templated transcription / DNA-templated transcription ...repressor LexA / SOS response / DNA-binding transcription repressor activity / protein-DNA complex / DNA replication / transcription cis-regulatory region binding / serine-type endopeptidase activity / DNA repair / negative regulation of DNA-templated transcription / DNA-templated transcription / DNA damage response / proteolysis / DNA binding / identical protein binding / cytosol
Similarity search - Function
LexA repressor, DNA-binding domain / Transcription regulator LexA / LexA DNA binding domain / Peptidase S24, LexA-like / Umud Fragment, subunit A / Umud Fragment, subunit A / LexA-like / Peptidase S24/S26A/S26B/S26C / Peptidase S24-like / LexA/Signal peptidase-like superfamily ...LexA repressor, DNA-binding domain / Transcription regulator LexA / LexA DNA binding domain / Peptidase S24, LexA-like / Umud Fragment, subunit A / Umud Fragment, subunit A / LexA-like / Peptidase S24/S26A/S26B/S26C / Peptidase S24-like / LexA/Signal peptidase-like superfamily / Ribbon / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Mainly Beta
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsLuo, Y. / Pfuetzner, R.A. / Mosimann, S. / Little, J.W. / J Strynadka, N.C.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2001
Title: Crystal structure of LexA: a conformational switch for regulation of self-cleavage.
Authors: Luo, Y. / Pfuetzner, R.A. / Mosimann, S. / Paetzel, M. / Frey, E.A. / Cherney, M. / Kim, B. / Little, J.W. / Strynadka, N.C.
History
DepositionJun 27, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 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 1.4Aug 16, 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: LEXA REPRESSOR
B: LEXA REPRESSOR


Theoretical massNumber of molelcules
Total (without water)29,8482
Polymers29,8482
Non-polymers00
Water30617
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)124.700, 43.700, 49.500
Angle α, β, γ (deg.)90.00, 109.50, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein LEXA REPRESSOR / Repressor lexA


Mass: 14924.055 Da / Num. of mol.: 2 / Fragment: C-Terminus, Residues 68-202 / Mutation: L89P,Q92W,E152A,K156A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: LexA / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7C2, repressor LexA
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 2.13 Å3/Da / Density % sol: 42.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 30% PEG 1500, 0.1 M MES buffer, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
130 %PEG15001reservoir
20.1 MMES1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Dec 20, 2000 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. all: 9700 / Num. obs: 9700 / % possible obs: 96.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.074 / Rsym value: 0.074 / Net I/σ(I): 18.2
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 3 % / Rmerge(I) obs: 0.431 / Mean I/σ(I) obs: 2.3 / Num. unique all: 486 / Rsym value: 0.431 / % possible all: 95.1
Reflection
*PLUS
Num. obs: 8960 / Num. measured all: 30913
Reflection shell
*PLUS
% possible obs: 95.1 % / Num. unique obs: 486

-
Processing

Software
NameVersionClassification
AMoREphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1JHC

1jhc


Resolution: 2.5→15 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.284 819 -RANDOM
Rwork0.22 ---
all-7992 --
obs-7992 90.5 %-
Refinement stepCycle: LAST / Resolution: 2.5→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1908 0 0 17 1925
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.52
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 15 Å / σ(F): 0 / Rfactor obs: 0.22 / Rfactor Rwork: 0.22 / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
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