[English] 日本語
Yorodumi
- PDB-5ywj: Global regulatory element SarX -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ywj
TitleGlobal regulatory element SarX
ComponentsHTH-type transcriptional regulator SarX
KeywordsTRANSCRIPTION / Global regulatory element / DNA-binding / transcriptional contral
Function / homologyTranscriptional regulator SarA/Rot / : / Transcriptional regulator SarA/Rot / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / regulation of DNA-templated transcription / DNA binding / cytoplasm / HTH-type transcriptional regulator SarX
Function and homology information
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.102 Å
AuthorsWang, Q.
Funding support China, 4items
OrganizationGrant numberCountry
National Natural Science Foundation of China31130018 China
National Natural Science Foundation of China31370732 China
National Natural Science Foundation of China31270014 China
National Natural Science Foundation of ChinaU1432107 China
CitationJournal: To Be Published
Title: Crystal structure of SarX from Staphylococcus aureus
Authors: Wang, Q.
History
DepositionNov 29, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 5, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: HTH-type transcriptional regulator SarX


Theoretical massNumber of molelcules
Total (without water)15,0301
Polymers15,0301
Non-polymers00
Water30617
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.392, 33.392, 230.930
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

-
Components

#1: Protein HTH-type transcriptional regulator SarX / Staphylococcal accessory regulator X


Mass: 15030.436 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (strain NCTC 8325) (bacteria)
Strain: NCTC 8325 / Gene: sarX, SAOUHSC_00674 / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: Q2G0D1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 2.14 Å3/Da / Density % sol: 42.56 %
Crystal growTemperature: 289.16 K / Method: vapor diffusion, sitting drop / Details: Bicine pH9.0, 1,4-Dioxane, PEG 20000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97774 Å
DetectorType: DECTRIS PILATUS3 X 1M / Detector: PIXEL / Date: Jun 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97774 Å / Relative weight: 1
ReflectionResolution: 2.1→57.74 Å / Num. obs: 8345 / % possible obs: 98.7 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.087 / Rsym value: 0.087 / Net I/σ(I): 8.19
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.221 / Num. unique obs: 557 / Rsym value: 0.221

-
Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
xia2data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HS5

5hs5


Resolution: 2.102→23.612 Å / SU ML: 0.25 / Cross valid method: NONE / σ(F): 1.4 / Phase error: 32.58
RfactorNum. reflection% reflection
Rfree0.2849 386 4.64 %
Rwork0.2472 --
obs0.2489 8323 98.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.102→23.612 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms820 0 0 17 837
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007830
X-RAY DIFFRACTIONf_angle_d1.0311123
X-RAY DIFFRACTIONf_dihedral_angle_d12.939289
X-RAY DIFFRACTIONf_chiral_restr0.074140
X-RAY DIFFRACTIONf_plane_restr0.003137
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1018-2.40560.30351300.22212578X-RAY DIFFRACTION100
2.4056-3.02990.33741290.29472612X-RAY DIFFRACTION100
3.0299-23.61320.26581270.23692747X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: 14.0315 Å / Origin y: 10.4895 Å / Origin z: 16.1537 Å
111213212223313233
T0.2788 Å2-0.0418 Å2-0.0117 Å2-0.2124 Å20.0028 Å2--0.2569 Å2
L2.7504 °20.1817 °2-1.4917 °2-3.7638 °2-2.6501 °2--8.3851 °2
S0.0772 Å °-0.0669 Å °-0.0288 Å °0.4889 Å °-0.1017 Å °0.1421 Å °-0.3483 Å °0.2451 Å °0.0238 Å °
Refinement TLS groupSelection details: all

+
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