[English] 日本語
Yorodumi
- PDB-1i4v: SOLUTION STRUCTURE OF THE UMUD' HOMODIMER -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1i4v
TitleSOLUTION STRUCTURE OF THE UMUD' HOMODIMER
ComponentsUMUD' PROTEIN
KeywordsHYDROLASE / SOS response / SOS mutagenesis / DNA repair / DNA polymerase V / DNA polymerase accessory protein / LexA repressor / lambda CI / signal peptidase / serine-lysine dyad / autocatalytic cleavage / serine protease
Function / homology
Function and homology information


DNA polymerase V complex / SOS response / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / translesion synthesis / ATP-dependent activity, acting on DNA / serine-type peptidase activity / single-stranded DNA binding / nucleic acid binding / DNA-directed DNA polymerase activity / DNA repair ...DNA polymerase V complex / SOS response / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / translesion synthesis / ATP-dependent activity, acting on DNA / serine-type peptidase activity / single-stranded DNA binding / nucleic acid binding / DNA-directed DNA polymerase activity / DNA repair / DNA damage response / regulation of DNA-templated transcription / proteolysis / DNA binding / identical protein binding / cytosol
Similarity search - Function
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 / Mainly Beta
Similarity search - Domain/homology
Protein UmuD / Protein UmuD
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / simulated annealing
AuthorsFerentz, A.E. / Walker, G.C. / Wagner, G.
CitationJournal: EMBO J. / Year: 2001
Title: Converting a DNA damage checkpoint effector (UmuD2C) into a lesion bypass polymerase (UmuD'2C).
Authors: Ferentz, A.E. / Walker, G.C. / Wagner, G.
History
DepositionFeb 23, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 22, 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: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: UMUD' PROTEIN
B: UMUD' PROTEIN


Theoretical massNumber of molelcules
Total (without water)24,6182
Polymers24,6182
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the least restraint violations,structures with the lowest energy
RepresentativeModel #1closest to the average

-
Components

#1: Protein UMUD' PROTEIN


Mass: 12308.985 Da / Num. of mol.: 2 / Mutation: G25A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: UMUD / Plasmid: PET5A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLYSS
References: UniProt: P04153, UniProt: P0AG11*PLUS, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111HNHA
1213D 15N-separated NOESY
1332D NOESY
1442D NOESY
1523D 13C-separated NOESY
1663D 15N-separated NOESY
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy

-
Sample preparation

Details
Solution-IDContentsSolvent system
10.9 mM UmuD' U-15N; 150 mM NaCl, 10 mM phosphate, pH 6.0, 1mM DTT, 0.1 mM EDTA95% H2O/5% D2O
21.3 mM UmuD' U-15N,13C; 150 mM NaCl, 20 mM phosphate, pH 6.0, 1 mM DTT, 0.1 mM EDTA95% H2O/5% D2O
31.5 mM UmuD' unlabeled; 150 mM NaCl, 20 mM phosphate, pH 6.0, 1 mM DTT, 0.1 mM EDTA95% H20, 5% D2O
41.4 mM UmuD' unlabeled; 150 mM NaCl, 20 mM phosphate, pH 6.0, 1 mM DTT, 0.1 mM EDTA100% D2O
50.5 mM UmuD' U-10% 13C; 150 mM NaCl, 20 mM phosphate, pH 6.0, 1 mM DTT, 0.1 mM EDTA100% D2O
62.7 mM UmuD' U-100% 2H,15N and 2.7 mM unlabeled UmuD'; 150 mM NaCl, 20 mM phosphate, pH 6.0, 1 mM DTT, 0.1 mM EDTA95% H20, 5% D2O
Sample conditionsIonic strength: 150 mM NaCl / pH: 6 / Pressure: ambient / Temperature: 303 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian UNITYPLUSVarianUNITYPLUS7501
Varian UNITYPLUSVarianUNITYPLUS4002
Bruker AMXBrukerAMX6003
Bruker AMXBrukerAMX5004
Varian VXRVarianVXR5005

-
Processing

NMR software
NameVersionDeveloperClassification
Felix97Molecular Simulations Inc.processing
XEASY1.3.9Bartels et aldata analysis
X-PLOR3.851Brungerrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations,structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

+
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