[English] 日本語
Yorodumi
- PDB-1qvu: Crystal structure of the multidrug binding transcriptional repres... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1qvu
TitleCrystal structure of the multidrug binding transcriptional repressor QacR bound to two drugs: ethidium and proflavine
ComponentsTranscriptional regulator qacR
KeywordsTRANSCRIPTION / QacR / multidrug binding protein / repressor / cooperative DNA binding
Function / homology
Function and homology information


DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / DNA binding
Similarity search - Function
Transcription regulator QacR, C-terminal / QacR-like protein, C-terminal region / DNA-binding HTH domain, TetR-type, conserved site / TetR-type HTH domain signature. / Tetracycline Repressor, domain 2 / Tetracyclin repressor-like, C-terminal domain superfamily / Tetracycline Repressor; domain 2 / Bacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type / TetR-type HTH domain profile. ...Transcription regulator QacR, C-terminal / QacR-like protein, C-terminal region / DNA-binding HTH domain, TetR-type, conserved site / TetR-type HTH domain signature. / Tetracycline Repressor, domain 2 / Tetracyclin repressor-like, C-terminal domain superfamily / Tetracycline Repressor; domain 2 / Bacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type / TetR-type HTH domain profile. / Homeodomain-like / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ETHIDIUM / PROFLAVIN / HTH-type transcriptional regulator QacR
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.96 Å
AuthorsSchumacher, M.A. / Miller, M.C. / Brennan, R.G.
CitationJournal: Embo J. / Year: 2004
Title: Structural mechanism of the simultaneous binding of two drugs to a multidrug-binding protein
Authors: Schumacher, M.A. / Miller, M.C. / Brennan, R.G.
History
DepositionAug 28, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Transcriptional regulator qacR
D: Transcriptional regulator qacR
A: Transcriptional regulator qacR
E: Transcriptional regulator qacR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,5846
Polymers92,0604
Non-polymers5242
Water00
1
B: Transcriptional regulator qacR
A: Transcriptional regulator qacR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,5544
Polymers46,0302
Non-polymers5242
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4340 Å2
ΔGint-16 kcal/mol
Surface area17570 Å2
MethodPISA
2
D: Transcriptional regulator qacR
E: Transcriptional regulator qacR


Theoretical massNumber of molelcules
Total (without water)46,0302
Polymers46,0302
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2950 Å2
ΔGint-22 kcal/mol
Surface area17590 Å2
MethodPISA
3
B: Transcriptional regulator qacR
A: Transcriptional regulator qacR
hetero molecules

B: Transcriptional regulator qacR
A: Transcriptional regulator qacR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,1088
Polymers92,0604
Non-polymers1,0474
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area11100 Å2
ΔGint-46 kcal/mol
Surface area32710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)171.800, 171.800, 94.590
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
DetailsQacR is a functional dimer

-
Components

#1: Protein
Transcriptional regulator qacR


Mass: 23015.088 Da / Num. of mol.: 4 / Fragment: QacR
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: QACR OR SAVP031 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A0N4
#2: Chemical ChemComp-ET / ETHIDIUM


Mass: 314.404 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H20N3
#3: Chemical ChemComp-PRL / PROFLAVIN


Mass: 209.247 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H11N3

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.79 Å3/Da / Density % sol: 67.55 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: ammonium sulfate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 12, 2002
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.96→121.48 Å / Num. all: 31274 / Num. obs: 31274 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 104.3 Å2 / Rsym value: 0.078
Reflection shellResolution: 2.96→3.02 Å / % possible all: 98.9

-
Processing

Software
NameVersionClassification
CNS1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1JT6

1jt6


Resolution: 2.96→121.48 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1386142.59 / Data cutoff high rms absF: 1386142.59 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.273 1500 5.1 %RANDOM
Rwork0.223 ---
all0.226 29566 --
obs0.223 29566 98.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 65.0678 Å2 / ksol: 0.368225 e/Å3
Displacement parametersBiso mean: 90.4 Å2
Baniso -1Baniso -2Baniso -3
1-6.13 Å20 Å20 Å2
2--6.13 Å20 Å2
3----12.27 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.47 Å0.43 Å
Refinement stepCycle: LAST / Resolution: 2.96→121.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6188 0 40 0 6228
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d20
X-RAY DIFFRACTIONc_improper_angle_d0.89
LS refinement shellResolution: 2.96→3.15 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.379 266 5.4 %
Rwork0.354 4632 -
obs--99.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3PF_PARAMPF_TOP
X-RAY DIFFRACTION4ETBR.PARAMETBR.TOP
X-RAY DIFFRACTION5ION.PARAMION.TOP

+
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://pdbjlvh1.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