[English] 日本語
Yorodumi
- PDB-6swf: Selenomethionine derivative of the REC domain of AraT, a response... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6swf
TitleSelenomethionine derivative of the REC domain of AraT, a response regulator from Geobacillus stearothermophilus
ComponentsTwo-component response regulator
KeywordsTRANSCRIPTION / Response regulator / two component sensing system / Geobacillus stearothermophilus / arabinan utilization system
Function / homology
Function and homology information


phosphorelay signal transduction system / sequence-specific DNA binding / DNA-binding transcription factor activity / cytoplasm
Similarity search - Function
CdaR, GGDEF-like domain / : / GGDEF-like domain / Transcription regulator HTH, AraC- type / HTH domain AraC-type, conserved site / Bacterial regulatory proteins, araC family signature. / Helix-turn-helix domain / DNA binding HTH domain, AraC-type / Bacterial regulatory proteins, araC family DNA-binding domain profile. / helix_turn_helix, arabinose operon control protein ...CdaR, GGDEF-like domain / : / GGDEF-like domain / Transcription regulator HTH, AraC- type / HTH domain AraC-type, conserved site / Bacterial regulatory proteins, araC family signature. / Helix-turn-helix domain / DNA binding HTH domain, AraC-type / Bacterial regulatory proteins, araC family DNA-binding domain profile. / helix_turn_helix, arabinose operon control protein / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Homeobox-like domain superfamily
Similarity search - Domain/homology
Two-component response regulator
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.601 Å
AuthorsLansky, S. / Lavid, N. / Shoham, Y. / Shoham, G.
CitationJournal: To Be Published
Title: Selenomethionine derivative of the REC domain of AraT, a response regulator from Geobacillus stearothermophilus
Authors: Lansky, S. / Lavid, N. / Shoham, Y. / Shoham, G.
History
DepositionSep 20, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 14, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Two-component response regulator
B: Two-component response regulator


Theoretical massNumber of molelcules
Total (without water)31,5762
Polymers31,5762
Non-polymers00
Water77543
1
A: Two-component response regulator


Theoretical massNumber of molelcules
Total (without water)15,7881
Polymers15,7881
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Two-component response regulator


Theoretical massNumber of molelcules
Total (without water)15,7881
Polymers15,7881
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.131, 32.892, 78.656
Angle α, β, γ (deg.)90.000, 97.290, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Two-component response regulator


Mass: 15788.048 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Gene: araT / Production host: Escherichia coli (E. coli) / References: UniProt: B3EYL7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.01 Å3/Da / Density % sol: 38.94 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 41% PPG 425 and 0.1 M Bis-Tris pH 6

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.98 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 7778 / % possible obs: 99.3 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.135 / Net I/σ(I): 13.3
Reflection shellResolution: 2.6→2.64 Å / Rmerge(I) obs: 0.525 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 765 / % possible all: 98.2

-
Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.601→39.01 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 37.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3253 725 9.37 %
Rwork0.2354 7016 -
obs0.2434 7741 99.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 143.55 Å2 / Biso mean: 30.0137 Å2 / Biso min: 7.01 Å2
Refinement stepCycle: final / Resolution: 2.601→39.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2108 0 0 43 2151
Biso mean---29.29 -
Num. residues----258
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.601-2.80140.35281460.2687137999
2.8014-3.08320.38041370.26971380100
3.0832-3.52910.34651430.245140299
3.5291-4.44530.29481250.2152142699
4.4453-39.010.30431740.2196142999

+
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