[English] 日本語
Yorodumi
- PDB-5yc9: Crystal structure of a Pseudomonas aeruginosa transcriptional reg... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5yc9
TitleCrystal structure of a Pseudomonas aeruginosa transcriptional regulator
ComponentsC-di-GMP-binding multidrug transporter transcriptional regulator BrlR
KeywordsTRANSCRIPTION / Pseudomonas aeruginosa / transcriptional regulator
Function / homology
Function and homology information


DNA-binding transcription activator activity / protein-DNA complex / transcription cis-regulatory region binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / DNA binding
Similarity search - Function
Integron-associated effector binding protein / Integron-associated effector binding protein / Bacterial transcription activator, effector binding / Bacterial transcription activator, effector binding domain / MerR family regulatory protein / Regulatory factor, effector binding domain superfamily / : / MerR HTH family regulatory protein / MerR-type HTH domain profile. / helix_turn_helix, mercury resistance ...Integron-associated effector binding protein / Integron-associated effector binding protein / Bacterial transcription activator, effector binding / Bacterial transcription activator, effector binding domain / MerR family regulatory protein / Regulatory factor, effector binding domain superfamily / : / MerR HTH family regulatory protein / MerR-type HTH domain profile. / helix_turn_helix, mercury resistance / MerR-type HTH domain / Putative DNA-binding domain superfamily
Similarity search - Domain/homology
C-di-GMP-binding multidrug transporter transcriptional regulator BrlR / Probable transcriptional regulator
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsHarikiran, R. / Rohan, S.
CitationJournal: To Be Published
Title: Crystal structure of a Pseudomonas aeruginosa transcriptional regulator
Authors: Harikiran, R. / Sundararajan, R. / Sharma, R.
History
DepositionSep 7, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 20, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: C-di-GMP-binding multidrug transporter transcriptional regulator BrlR
B: C-di-GMP-binding multidrug transporter transcriptional regulator BrlR
C: C-di-GMP-binding multidrug transporter transcriptional regulator BrlR
D: C-di-GMP-binding multidrug transporter transcriptional regulator BrlR


Theoretical massNumber of molelcules
Total (without water)133,7594
Polymers133,7594
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14320 Å2
ΔGint-68 kcal/mol
Surface area53420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.642, 111.642, 261.137
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

-
Components

#1: Protein
C-di-GMP-binding multidrug transporter transcriptional regulator BrlR / Multidrug-efflux transporter 1 regulator / Transcriptional regulator


Mass: 33439.750 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Gene: bmrR, brlR, AO964_25340, AOY09_00728, CAZ10_02115, CGU42_14110, CWI21_27955, PAERUG_E15_London_28_01_14_00871, RW109_RW109_06470
Production host: Escherichia coli (E. coli) / References: UniProt: A0A069Q416, UniProt: Q9HUT5*PLUS

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.51 Å3/Da / Density % sol: 69.31 %
Description: the entry contains Friedel pairs in I_Plus/Minus columns
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 10% v/v 1,4-Dioxane, 0.1 M MES pH 6.5, 1.6 M Ammonium sulfate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.98 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 8, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.9→35 Å / Num. obs: 60294 / % possible obs: 100 % / Redundancy: 7.9 % / Net I/σ(I): 18.71
Reflection shellResolution: 2.9→2.95 Å

-
Processing

Software
NameVersionClassification
PHENIX(dev_2875)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→34.323 Å / Cross valid method: FREE R-VALUE / σ(F): 56.84 / Phase error: 33.88 / Stereochemistry target values: TWIN_LSQ_F
Details: the entry contains Friedel pairs in I_Plus/Minus columns
RfactorNum. reflection% reflection
Rfree0.3069 3949 6.55 %
Rwork0.268 --
obs0.2715 60294 74.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.9→34.323 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8290 0 0 0 8290
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9058-2.95590.4168340.3862577X-RAY DIFFRACTION14
2.9559-3.00960.4219510.3621811X-RAY DIFFRACTION20
3.0096-3.06740.3738700.37871186X-RAY DIFFRACTION30
3.0674-3.12990.4135890.35071703X-RAY DIFFRACTION43
3.1299-3.19790.40791100.34812083X-RAY DIFFRACTION51
3.1979-3.27220.39661260.32242146X-RAY DIFFRACTION54
3.2722-3.35390.34481290.31862307X-RAY DIFFRACTION58
3.3539-3.44440.33381450.31452522X-RAY DIFFRACTION64
3.4444-3.54550.34121880.2862923X-RAY DIFFRACTION73
3.5455-3.65980.35211950.28183348X-RAY DIFFRACTION83
3.6598-3.79030.27172230.26873696X-RAY DIFFRACTION91
3.7903-3.94160.25242100.27313735X-RAY DIFFRACTION93
3.9416-4.12050.35552120.26373763X-RAY DIFFRACTION94
4.1205-4.3370.30992120.25323743X-RAY DIFFRACTION94
4.337-4.60760.30122150.22843782X-RAY DIFFRACTION94
4.6076-4.96160.252140.21553741X-RAY DIFFRACTION94
4.9616-5.45770.27432120.2533793X-RAY DIFFRACTION94
5.4577-6.23990.34222260.28363796X-RAY DIFFRACTION94
6.2399-7.83360.24992140.26793722X-RAY DIFFRACTION94
7.8336-28.17930.29411970.25673605X-RAY DIFFRACTION90

+
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