[English] 日本語
Yorodumi
- PDB-2hxr: Structure of the ligand binding domain of E. coli CynR, a transcr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2hxr
TitleStructure of the ligand binding domain of E. coli CynR, a transcriptional regulator controlling cyanate metabolism
ComponentsHTH-type transcriptional regulator cynR
KeywordsTRANSCRIPTION / CynR transcriptional regulator LysR crystal structure / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


protein-DNA complex / DNA-binding transcription factor activity / regulation of DNA-templated transcription / DNA binding / cytoplasm
Similarity search - Function
HTH-type transcriptional regulator CynR, PBP2 domain / D-Maltodextrin-Binding Protein; domain 2 - #290 / LysR, substrate-binding / LysR substrate binding domain / LysR-type HTH domain profile. / Transcription regulator HTH, LysR / Bacterial regulatory helix-turn-helix protein, lysR family / D-Maltodextrin-Binding Protein; domain 2 / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily ...HTH-type transcriptional regulator CynR, PBP2 domain / D-Maltodextrin-Binding Protein; domain 2 - #290 / LysR, substrate-binding / LysR substrate binding domain / LysR-type HTH domain profile. / Transcription regulator HTH, LysR / Bacterial regulatory helix-turn-helix protein, lysR family / D-Maltodextrin-Binding Protein; domain 2 / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
HTH-type transcriptional regulator CynR
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.05 Å
AuthorsSinger, A.U. / Cuff, M.E. / Evdokimova, E. / Kagan, O. / Joachimiak, A. / Edwards, A.M. / Savchenko, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The structure of CynR, a transcriptional regulator, both in the presence and absence of sodium azide, its activator ligand
Authors: Singer, A.U. / Evdokimova, E. / Cuff, M.E. / Kagan, O. / Edwards, A.M. / Joachimiak, A. / Savchenko, A.
History
DepositionAug 3, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 22, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: HTH-type transcriptional regulator cynR
B: HTH-type transcriptional regulator cynR


Theoretical massNumber of molelcules
Total (without water)52,8122
Polymers52,8122
Non-polymers00
Water6,269348
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2440 Å2
ΔGint-15 kcal/mol
Surface area17600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.913, 98.555, 62.236
Angle α, β, γ (deg.)90.00, 104.35, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein HTH-type transcriptional regulator cynR / Cyn operon transcriptional activator


Mass: 26405.803 Da / Num. of mol.: 2 / Fragment: residues 63-299
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: cynR / Plasmid: p15Tv-lic / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P27111
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 348 / 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: 2.47 Å3/Da / Density % sol: 50.24 %
Description: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.2M Sodium formate, 22% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97885, 0.97874
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 22, 2005
RadiationMonochromator: Si 111 Channel / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.978851
20.978741
ReflectionResolution: 2.05→20 Å / Num. all: 57793 / Num. obs: 57793 / % possible obs: 89.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Biso Wilson estimate: 3.1 Å2 / Rsym value: 0.066 / Net I/σ(I): 13.8
Reflection shellResolution: 2.05→2.12 Å / Redundancy: 2.1 % / Mean I/σ(I) obs: 2.9 / Num. unique all: 4233 / Rsym value: 0.269 / % possible all: 65.9

-
Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXCDphasing
SHELXDphasing
SHELXEmodel building
MLPHAREphasing
RefinementMethod to determine structure: SAD / Resolution: 2.05→19.98 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2196467.43 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1.5 / Stereochemistry target values: Engh & Huber / Details: THE FRIEDEL PAIRS WERE USED FOR PHASING
RfactorNum. reflection% reflectionSelection details
Rfree0.256 2780 4.9 %RANDOM
Rwork0.239 ---
all0.241 57143 --
obs0.239 56855 89.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 51.6945 Å2 / ksol: 0.334972 e/Å3
Displacement parametersBiso mean: 32.8 Å2
Baniso -1Baniso -2Baniso -3
1-13.53 Å20 Å22.02 Å2
2---2.82 Å20 Å2
3----10.71 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.28 Å0.28 Å
Refinement stepCycle: LAST / Resolution: 2.05→19.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3123 0 0 348 3471
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.87
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2.05→2.18 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.325 380 5.2 %
Rwork0.301 6929 -
obs--69.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3ion.param

+
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