[English] 日本語
Yorodumi
- PDB-4hqm: The crystal structure of QsrR-menadione complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4hqm
TitleThe crystal structure of QsrR-menadione complex
ComponentsQsrR protein
KeywordsTRANSCRIPTION regulator / menadione-modified protein / DNA
Function / homologyWinged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha / 2-methylnaphthalene-1,4-diol / :
Function and homology information
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsJi, Q. / Zhang, L. / Jones, M.B. / Sun, F. / Deng, X. / Liang, H. / Brugarolas, P. / Gao, N. / Peterson, S.N. / Lan, L. ...Ji, Q. / Zhang, L. / Jones, M.B. / Sun, F. / Deng, X. / Liang, H. / Brugarolas, P. / Gao, N. / Peterson, S.N. / Lan, L. / Bae, T. / He, C.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Molecular mechanism of quinone signaling mediated through S-quinonization of a YodB family repressor QsrR.
Authors: Ji, Q. / Zhang, L. / Jones, M.B. / Sun, F. / Deng, X. / Liang, H. / Cho, H. / Brugarolas, P. / Gao, Y.N. / Peterson, S.N. / Lan, L. / Bae, T. / He, C.
History
DepositionOct 25, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2013Provider: repository / Type: Initial release
Revision 1.1May 22, 2013Group: Database references

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: QsrR protein
B: QsrR protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4924
Polymers26,1442
Non-polymers3482
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2950 Å2
ΔGint-29 kcal/mol
Surface area10650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.758, 124.758, 30.633
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number168
Space group name H-MP6

-
Components

#1: Protein QsrR protein


Mass: 13071.968 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: I3FJN1
#2: Chemical ChemComp-17Z / 2-methylnaphthalene-1,4-diol / Menadione, bound form / Menadione


Mass: 174.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H10O2
Sequence detailsTHE AUTHOR STATES THAT THE RESIDUES AT POSITIONS 30 AND 33 ARE CONSISTENT WITH SER.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.63 Å3/Da / Density % sol: 53.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M NaCl, 0.1 M Tris.HCl, pH 8.5, 25% (w/v) polyethylene glycol 3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 25, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.55→20 Å / Num. obs: 8886

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
PHENIX(phenix.refine: 1.7.2_869)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.55→19.405 Å / SU ML: 0.99 / σ(F): 1.34 / Phase error: 38.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2962 418 4.7 %
Rwork0.284 --
obs0.2846 8886 96.48 %
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.476 Å2 / ksol: 0.311 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.0973 Å20 Å2-0 Å2
2--0.0973 Å20 Å2
3----0.1946 Å2
Refinement stepCycle: LAST / Resolution: 2.55→19.405 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1595 0 26 0 1621
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0211659
X-RAY DIFFRACTIONf_angle_d2.5452256
X-RAY DIFFRACTIONf_dihedral_angle_d21.843606
X-RAY DIFFRACTIONf_chiral_restr0.186256
X-RAY DIFFRACTIONf_plane_restr0.025273
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5498-2.91770.46521470.40712809X-RAY DIFFRACTION98
2.9177-3.6720.3561350.33962839X-RAY DIFFRACTION98
3.672-19.40580.24761360.24532820X-RAY DIFFRACTION94

+
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