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

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1jtx
TitleCrystal structure of the multidrug binding transcriptional regulator QacR bound to crystal violet
ComponentsHYPOTHETICAL TRANSCRIPTIONAL REGULATOR IN QACA 5'REGION
KeywordsTRANSCRIPTION / multidrug binding / repressor / S. aureus / QacA / QacR / multidrug recognition
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 ...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
CRYSTAL VIOLET / HTH-type transcriptional regulator QacR
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.85 Å
AuthorsSchumacher, M.A. / Miller, M.C. / Grkovic, S. / Brown, M.H. / Skurray, R.A. / Brennan, R.G.
CitationJournal: Science / Year: 2001
Title: Structural mechanisms of QacR induction and multidrug recognition.
Authors: Schumacher, M.A. / Miller, M.C. / Grkovic, S. / Brown, M.H. / Skurray, R.A. / Brennan, R.G.
History
DepositionAug 22, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 7, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations / Category: database_2 / 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
Revision 1.4Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: HYPOTHETICAL TRANSCRIPTIONAL REGULATOR IN QACA 5'REGION
D: HYPOTHETICAL TRANSCRIPTIONAL REGULATOR IN QACA 5'REGION
A: HYPOTHETICAL TRANSCRIPTIONAL REGULATOR IN QACA 5'REGION
E: HYPOTHETICAL TRANSCRIPTIONAL REGULATOR IN QACA 5'REGION
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,61029
Polymers91,9324
Non-polymers2,67825
Water1,15364
1
B: HYPOTHETICAL TRANSCRIPTIONAL REGULATOR IN QACA 5'REGION
A: HYPOTHETICAL TRANSCRIPTIONAL REGULATOR IN QACA 5'REGION
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,58716
Polymers45,9662
Non-polymers1,62114
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6060 Å2
ΔGint-154 kcal/mol
Surface area18110 Å2
MethodPISA
2
D: HYPOTHETICAL TRANSCRIPTIONAL REGULATOR IN QACA 5'REGION
E: HYPOTHETICAL TRANSCRIPTIONAL REGULATOR IN QACA 5'REGION
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,02313
Polymers45,9662
Non-polymers1,05711
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4710 Å2
ΔGint-151 kcal/mol
Surface area17940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)172.900, 172.900, 95.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
DetailsThe natural oligmeric state is a dimer- there are two dimers in the ASU

-
Components

#1: Protein
HYPOTHETICAL TRANSCRIPTIONAL REGULATOR IN QACA 5'REGION / QACR REPRESSOR / ORF 188


Mass: 22983.023 Da / Num. of mol.: 4 / Mutation: C72A, C141S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Plasmid: pSK / Production host: Escherichia coli (E. coli) / Strain (production host): DH5a / References: UniProt: P0A0N4
#2: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CVI / CRYSTAL VIOLET


Mass: 372.526 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H30N3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / 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: 3.87 Å3/Da / Density % sol: 68.18 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Ammonium sulphate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
1200 mMglycine1drop
215 mg/mlprotein1drop
325 mMTris1reservoirpH7.5
450 mMimidazole1drop
5300 mM1dropNaCl
65 %glycerol1drop

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 20, 2000 / Details: mirrors
RadiationMonochromator: monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.85→63.97 Å / Num. all: 34304 / Num. obs: 34304 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.9 % / Biso Wilson estimate: 62.7 Å2 / Rmerge(I) obs: 0.07 / Rsym value: 0.064 / Net I/σ(I): 8.5
Reflection shellResolution: 2.85→2.92 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.449 / Mean I/σ(I) obs: 1.7 / Num. unique all: 2508 / Rsym value: 0.449 / % possible all: 100
Reflection
*PLUS
Num. measured all: 340448 / Rmerge(I) obs: 0.064

-
Processing

Software
NameVersionClassification
CNSrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1JUS

1jus


Resolution: 2.85→63.97 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1728986.14 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh and Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.284 3417 10 %RANDOM
Rwork0.227 ---
all-34220 --
obs-34220 100 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 65.2069 Å2 / ksol: 0.359843 e/Å3
Displacement parametersBiso mean: 77 Å2
Baniso -1Baniso -2Baniso -3
1-1.62 Å20 Å20 Å2
2--1.62 Å20 Å2
3----3.24 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.48 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.52 Å0.41 Å
Refinement stepCycle: LAST / Resolution: 2.85→63.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6188 0 148 64 6400
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d19.2
X-RAY DIFFRACTIONc_improper_angle_d0.84
X-RAY DIFFRACTIONc_mcbond_it2.451.5
X-RAY DIFFRACTIONc_mcangle_it4.092
X-RAY DIFFRACTIONc_scbond_it3.522
X-RAY DIFFRACTIONc_scangle_it5.52.5
LS refinement shellResolution: 2.85→3.03 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.398 556 9.9 %
Rwork0.354 5052 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
X-RAY DIFFRACTION5CVI.PARAMCV.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.228 / Rfactor Rfree: 0.286
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 77 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg2.43
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg19.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.84
X-RAY DIFFRACTIONc_mcbond_it2.451.5
X-RAY DIFFRACTIONc_scbond_it3.522
X-RAY DIFFRACTIONc_mcangle_it4.092
X-RAY DIFFRACTIONc_scangle_it5.52.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.398 / % reflection Rfree: 9.9 % / Rfactor Rwork: 0.354

+
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