[English] 日本語
Yorodumi
- PDB-8hig: Co-crystal structure of C-terminal DNA binding domain of Saccharo... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8hig
TitleCo-crystal structure of C-terminal DNA binding domain of Saccharopolyspora erythraea GlnR in complex with its cognate promoter DNA
Components
  • DNA (5'-D(*AP*CP*GP*TP*AP*AP*CP*AP*TP*CP*GP*CP*GP*GP*TP*AP*AP*CP*AP*C)-3')
  • DNA (5'-D(*GP*TP*GP*TP*TP*AP*CP*CP*GP*CP*GP*AP*TP*GP*TP*TP*AP*CP*GP*T)-3')
  • DNA-binding response OmpR family regulator
KeywordsTRANSCRIPTION/DNA / Transcription factor / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


phosphorelay response regulator activity / protein-DNA complex / transcription cis-regulatory region binding / negative regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / cytosol
Similarity search - Function
: / Transcription regulator GlnR, N-terminal domain / 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 / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / Transcriptional regulator
Similarity search - Component
Biological speciesSaccharopolyspora erythraea NRRL 2338 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.329 Å
AuthorsLin, W. / Xu, J.C. / Zhang, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81903526 China
CitationJournal: To Be Published
Title: Co-crystal structure of C-terminal DNA binding domain of Saccharopolyspora erythraea GlnR in complex with its cognate promoter DNA
Authors: Lin, W. / Xu, J.C. / Zhang, Y.
History
DepositionNov 20, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 22, 2023Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA-binding response OmpR family regulator
B: DNA-binding response OmpR family regulator
D: DNA (5'-D(*AP*CP*GP*TP*AP*AP*CP*AP*TP*CP*GP*CP*GP*GP*TP*AP*AP*CP*AP*C)-3')
C: DNA (5'-D(*GP*TP*GP*TP*TP*AP*CP*CP*GP*CP*GP*AP*TP*GP*TP*TP*AP*CP*GP*T)-3')


Theoretical massNumber of molelcules
Total (without water)67,5254
Polymers67,5254
Non-polymers00
Water86548
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5620 Å2
ΔGint-29 kcal/mol
Surface area14830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.279, 46.279, 366.859
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11C-108-

HOH

-
Components

#1: Protein DNA-binding response OmpR family regulator / Transcriptional regulator


Mass: 27628.424 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharopolyspora erythraea NRRL 2338 (bacteria)
Strain: NRRL 2338 / Gene: glnR / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A4FQD5
#2: DNA chain DNA (5'-D(*AP*CP*GP*TP*AP*AP*CP*AP*TP*CP*GP*CP*GP*GP*TP*AP*AP*CP*AP*C)-3')


Mass: 6111.983 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Saccharopolyspora erythraea NRRL 2338 (bacteria)
#3: DNA chain DNA (5'-D(*GP*TP*GP*TP*TP*AP*CP*CP*GP*CP*GP*AP*TP*GP*TP*TP*AP*CP*GP*T)-3')


Mass: 6155.975 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Saccharopolyspora erythraea NRRL 2338 (bacteria)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / 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: 1.68 Å3/Da / Density % sol: 26.76 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 0.1M Bis-Tris pH5.7, 25% PEG3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 2, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.329→50 Å / Num. obs: 19059 / % possible obs: 90.7 % / Redundancy: 5.1 % / CC1/2: 0.9 / Net I/σ(I): 11.146
Reflection shellResolution: 2.34→2.38 Å / Rmerge(I) obs: 1.72 / Mean I/σ(I) obs: 2.034 / Num. unique obs: 569 / CC1/2: 0.107 / Rsym value: 1.62 / % possible all: 78.3

-
Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.329→39.842 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.46 / Phase error: 35.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3247 1325 9.98 %
Rwork0.2586 11948 -
obs0.2654 13273 63.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 79.48 Å2 / Biso mean: 23.4535 Å2 / Biso min: 1.45 Å2
Refinement stepCycle: final / Resolution: 2.329→39.842 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1493 812 0 48 2353
Biso mean---17.61 -
Num. residues----228
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.3295-2.42270.4417610.36656928
2.4227-2.5330.4601740.365266533
2.533-2.66650.3779870.377982040
2.6665-2.83350.41761120.376199549
2.8335-3.05220.44071510.3483134065
3.0522-3.35920.33561890.2776164880
3.3592-3.8450.32771900.2419173482
3.845-4.84290.30272110.2095188490
4.8429-39.8420.24382500.2097229399

+
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