[English] 日本語
Yorodumi
- PDB-8gc6: 1.30 Angstroem crystal structure of the N-terminal domain of BqsR... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8gc6
Title1.30 Angstroem crystal structure of the N-terminal domain of BqsR from Pseudomonas aeruginosa
ComponentsResponse regulator protein CarR
KeywordsTRANSCRIPTION / iron / regulator / two-component / biofilm
Function / homology
Function and homology information


phosphorelay response regulator activity / protein-DNA complex / response to calcium ion / transcription cis-regulatory region binding / regulation of DNA-templated transcription / cytosol
Similarity search - Function
OmpR/PhoB-type DNA-binding domain / Transcriptional regulatory protein, C terminal / OmpR/PhoB-type DNA-binding domain profile. / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein WalR-like / Signal transduction response regulator, C-terminal effector / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. ...OmpR/PhoB-type DNA-binding domain / Transcriptional regulatory protein, C terminal / OmpR/PhoB-type DNA-binding domain profile. / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein WalR-like / Signal transduction response regulator, C-terminal effector / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Response regulator protein CarR
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsParedes, A. / Smith, A.T.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM133497 United States
Howard Hughes Medical Institute (HHMI)GT15765 United States
CitationJournal: To Be Published
Title: 1.30 Angstroem crystal structure of the N-terminal domain of BqsR from Pseudomonas aeruginosa
Authors: Paredes, A. / Smith, A.T.
History
DepositionMar 1, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Response regulator protein CarR


Theoretical massNumber of molelcules
Total (without water)13,4741
Polymers13,4741
Non-polymers00
Water1,910106
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.740, 46.740, 111.160
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

-
Components

#1: Protein Response regulator protein CarR


Mass: 13474.474 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: carR, PA2657 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9I0I1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / 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: 2.25 Å3/Da / Density % sol: 45.4 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 1 M sodium/potassium phosphate, pH 8.2

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 27, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.3→29.04 Å / Num. obs: 31130 / % possible obs: 99.7 % / Redundancy: 7.1 % / Biso Wilson estimate: 16.62 Å2 / CC1/2: 0.999 / Net I/σ(I): 17.7
Reflection shellResolution: 1.3→1.32 Å / Num. unique obs: 1428 / CC1/2: 0.508

-
Processing

Software
NameVersionClassification
PHENIX1.15_3459refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→29.04 Å / SU ML: 0.116 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.0967
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1751 1527 4.92 %
Rwork0.158 29505 -
obs0.1588 31032 99.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.36 Å2
Refinement stepCycle: LAST / Resolution: 1.3→29.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms950 0 0 106 1056
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0133969
X-RAY DIFFRACTIONf_angle_d1.48281319
X-RAY DIFFRACTIONf_chiral_restr0.1247150
X-RAY DIFFRACTIONf_plane_restr0.0093172
X-RAY DIFFRACTIONf_dihedral_angle_d12.5938359
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.340.30621320.32042486X-RAY DIFFRACTION94.14
1.34-1.390.30011580.27522591X-RAY DIFFRACTION99.67
1.39-1.450.26671320.21692650X-RAY DIFFRACTION99.89
1.45-1.510.18691330.17342664X-RAY DIFFRACTION99.89
1.51-1.590.17761150.14042675X-RAY DIFFRACTION99.96
1.59-1.690.15041330.12282675X-RAY DIFFRACTION100
1.69-1.820.15391300.12682686X-RAY DIFFRACTION100
1.82-20.17321610.12922679X-RAY DIFFRACTION100
2-2.290.16881430.13472708X-RAY DIFFRACTION100
2.29-2.890.16641410.16112766X-RAY DIFFRACTION99.97
2.89-29.040.16541490.16212925X-RAY DIFFRACTION99.87

+
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