[English] 日本語
Yorodumi
- PDB-1us6: Crystal structure of the quorum-sensing protein TraM from Agrobac... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1us6
TitleCrystal structure of the quorum-sensing protein TraM from Agrobacterium tumefaciens at 1.65 Ang. resolution
ComponentsTRANSCRIPTIONAL REPRESSOR TRAM
KeywordsTRANSCRIPTION REPRESSOR / NEGATIVE REGULATOR / QUORUM-SENSING / CONJUGATION / TRANSCRIPTI REGULATION / REPRESSOR / PLASMID.
Function / homologyTranscriptional repressor TraM / Transcriptional repressor TraM superfamily / Prokaryotic Transcriptional repressor TraM / HR1 repeat / Helix Hairpins / negative regulation of DNA-templated transcription / Orthogonal Bundle / Mainly Alpha / Transcriptional repressor TraM
Function and homology information
Biological speciesAGROBACTERIUM TUMEFACIENS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.65 Å
AuthorsVannini, A. / Di Marco, S.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Crystal Structure of the Quorum-Sensing Protein Tram and its Interaction with the Transcriptional Regulator Trar
Authors: Vannini, A. / Volpari, C. / Di Marco, S.
History
DepositionNov 18, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 25, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: TRANSCRIPTIONAL REPRESSOR TRAM
B: TRANSCRIPTIONAL REPRESSOR TRAM


Theoretical massNumber of molelcules
Total (without water)22,8302
Polymers22,8302
Non-polymers00
Water3,909217
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)77.809, 47.432, 47.621
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein TRANSCRIPTIONAL REPRESSOR TRAM / TRAM


Mass: 11415.203 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) AGROBACTERIUM TUMEFACIENS (bacteria) / Description: SYNTHETIC GENE / Plasmid: PT7.7 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q57471
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 217 / Source method: isolated from a natural source / Formula: H2O
Compound detailsFUNCTION: NEGATIVELY REGULATES CONJUGATION AND TRA GENES EXPRESSION BY ANTAGONIZING TRAR/AAI ...FUNCTION: NEGATIVELY REGULATES CONJUGATION AND TRA GENES EXPRESSION BY ANTAGONIZING TRAR/AAI DEPENDENT ACTIVATION.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.92 Å3/Da / Density % sol: 36.09 %
Crystal growpH: 8.5 / Details: pH 8.50

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9611
DetectorType: ADSC CCD / Detector: CCD / Date: Jun 21, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9611 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 20190 / % possible obs: 98 % / Redundancy: 3 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 7

-
Processing

Software
NameClassification
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MAD / Resolution: 1.65→50 Å / SU B: 3.795 / SU ML: 0.127 / Cross valid method: THROUGHOUT / ESU R: 0.14 / ESU R Free: 0.134
RfactorNum. reflection% reflectionSelection details
Rfree0.26 1028 5 %RANDOM
Rwork0.21 ---
obs0.21 19120 92 %-
Displacement parametersBiso mean: 19.803 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å20 Å20 Å2
2--1.08 Å20 Å2
3----1.2 Å2
Refinement stepCycle: LAST / Resolution: 1.65→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1483 0 0 217 1700

+
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