[English] 日本語
Yorodumi
- PDB-6hob: TRANSCRIPTIONAL REPRESSOR ETHR FROM MYCOBACTERIUM TUBERCULOSIS IN... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6hob
TitleTRANSCRIPTIONAL REPRESSOR ETHR FROM MYCOBACTERIUM TUBERCULOSIS IN COMPLEX WITH BDM44831
ComponentsHTH-type transcriptional regulator EthR
KeywordsDNA BINDING PROTEIN / HELIX-TURN-HELIX / TETR-FAMILY / COMPLEX / INHIBITOR / DRUG DESIGN / TUBERCULOSIS / ETHIONAMIDE
Function / homology
Function and homology information


regulation of DNA-templated transcription / DNA binding
Similarity search - Function
: / Transcriptional regulator EthR, C-terminal domain / 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 ...: / Transcriptional regulator EthR, C-terminal domain / 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
Chem-GJ5 / HTH-type transcriptional regulator EthR
Similarity search - Component
Biological speciesMycobacterium tuberculosis CDC1551 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsWintjens, R. / Wohlkonig, A.
CitationJournal: Biochim Biophys Acta Proteins Proteom / Year: 2018
Title: A comprehensive analysis of the protein-ligand interactions in crystal structures of Mycobacterium tuberculosis EthR.
Authors: Tanina, A. / Wohlkonig, A. / Soror, S.H. / Flipo, M. / Villemagne, B. / Prevet, H. / Deprez, B. / Moune, M. / Peree, H. / Meyer, F. / Baulard, A.R. / Willand, N. / Wintjens, R.
History
DepositionSep 17, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 26, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 23, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 24, 2024Group: 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 EthR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2842
Polymers24,9281
Non-polymers3561
Water95553
1
A: HTH-type transcriptional regulator EthR
hetero molecules

A: HTH-type transcriptional regulator EthR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,5694
Polymers49,8562
Non-polymers7132
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area2680 Å2
ΔGint-21 kcal/mol
Surface area16950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.978, 121.978, 33.629
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-417-

HOH

21A-449-

HOH

-
Components

#1: Protein HTH-type transcriptional regulator EthR


Mass: 24927.980 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis CDC1551 (bacteria)
Gene: ethR, etaR, MT3970 / Variant: CDC 1551 / Oshkosh / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P9WMC0
#2: Chemical ChemComp-GJ5 / 4-[2-(2-methylpropyl)-1,3-thiazol-4-yl]-~{N}-[3,3,3-tris(fluoranyl)propyl]benzamide


Mass: 356.406 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H19F3N2OS
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 2.41 Å3/Da / Density % sol: 49.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.7 / Details: 1.4-1.6 ammonium sulfate, 15% glycerol, 100 mM MES

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 6, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→38.57 Å / Num. obs: 23495 / % possible obs: 97.4 % / Redundancy: 12.2 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 27.8
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 8.9 % / Rmerge(I) obs: 0.462 / Mean I/σ(I) obs: 4.9 / Num. unique obs: 2791 / % possible all: 83.5

-
Processing

Software
NameVersionClassification
REFMAC5.8.0232refinement
iMOSFLMdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1U9N

1u9n


Resolution: 1.8→38.57 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.94 / SU B: 2.188 / SU ML: 0.068 / Cross valid method: THROUGHOUT / ESU R: 0.106 / ESU R Free: 0.104 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21258 1173 5 %RANDOM
Rwork0.18264 ---
obs0.18415 22285 97.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 24.15 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å2-0 Å2-0 Å2
2--0 Å2-0 Å2
3----0.01 Å2
Refinement stepCycle: 1 / Resolution: 1.8→38.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1490 0 24 53 1567
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0131546
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171427
X-RAY DIFFRACTIONr_angle_refined_deg1.8341.6642109
X-RAY DIFFRACTIONr_angle_other_deg1.5941.5873283
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0025190
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.29221.39586
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.92515240
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9041513
X-RAY DIFFRACTIONr_chiral_restr0.090.2207
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021751
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02344
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.3252.364763
X-RAY DIFFRACTIONr_mcbond_other2.3252.362762
X-RAY DIFFRACTIONr_mcangle_it3.1333.535952
X-RAY DIFFRACTIONr_mcangle_other3.1313.537953
X-RAY DIFFRACTIONr_scbond_it3.5742.742783
X-RAY DIFFRACTIONr_scbond_other3.5742.743781
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.413.951158
X-RAY DIFFRACTIONr_long_range_B_refined6.4628.0151780
X-RAY DIFFRACTIONr_long_range_B_other6.4427.9391771
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.801→1.848 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 65 -
Rwork0.229 1240 -
obs--74.83 %

+
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