[English] 日本語
Yorodumi
- PDB-5n1i: unliganded form of the Mycobacterium tuberculosis repressor EthR2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5n1i
Titleunliganded form of the Mycobacterium tuberculosis repressor EthR2
ComponentsProbable transcriptional regulatory protein
KeywordsDNA BINDING PROTEIN / Repressor / EthR / TetR protein family.
Function / homology
Function and homology information


transcription cis-regulatory region binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription / plasma membrane
Similarity search - Function
: / Tetracyclin repressor-like, C-terminal domain / : / Tetracyclin repressor-like, C-terminal domain superfamily / Bacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type / TetR-type HTH domain profile. / Homeobox-like domain superfamily
Similarity search - Domain/homology
Probable transcriptional regulatory protein
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsWintjens, R. / Wohlkonig, A.
Citation
Journal: Science / Year: 2017
Title: Reversion of antibiotic resistance in Mycobacterium tuberculosis by spiroisoxazoline SMARt-420.
Authors: Blondiaux, N. / Moune, M. / Desroses, M. / Frita, R. / Flipo, M. / Mathys, V. / Soetaert, K. / Kiass, M. / Delorme, V. / Djaout, K. / Trebosc, V. / Kemmer, C. / Wintjens, R. / Wohlkonig, A. ...Authors: Blondiaux, N. / Moune, M. / Desroses, M. / Frita, R. / Flipo, M. / Mathys, V. / Soetaert, K. / Kiass, M. / Delorme, V. / Djaout, K. / Trebosc, V. / Kemmer, C. / Wintjens, R. / Wohlkonig, A. / Antoine, R. / Huot, L. / Hot, D. / Coscolla, M. / Feldmann, J. / Gagneux, S. / Locht, C. / Brodin, P. / Gitzinger, M. / Deprez, B. / Willand, N. / Baulard, A.R.
#1: Journal: Biochem. Biophys. Res. Commun. / Year: 2017
Title: Structural analysis of the interaction between spiroisoxazoline SMARt-420 and the Mycobacterium tuberculosis repressor EthR2.
Authors: Wohlkonig, A. / Remaut, H. / Moune, M. / Tanina, A. / Meyer, F. / Desroses, M. / Steyaert, J. / Willand, N. / Baulard, A.R. / Wintjens, R.
History
DepositionFeb 6, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 26, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2017Group: Database references / Category: citation
Item: _citation.journal_id_CSD / _citation.journal_volume ..._citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Feb 15, 2023Group: Database references / Category: database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.4Jan 29, 2025Group: Advisory / Structure summary / Category: pdbx_database_PDB_obs_spr / pdbx_entry_details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Probable transcriptional regulatory protein
B: Probable transcriptional regulatory protein


Theoretical massNumber of molelcules
Total (without water)48,2452
Polymers48,2452
Non-polymers00
Water724
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2860 Å2
ΔGint-28 kcal/mol
Surface area17250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.850, 74.470, 89.520
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: _ / Auth seq-ID: 12 - 201 / Label seq-ID: 32 - 221

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

-
Components

#1: Protein Probable transcriptional regulatory protein / TetR family transcriptional regulator / transcriptional regulatory protein EthR2


Mass: 24122.570 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: PURIFICATION TAG: RESIDUE 1-20
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Gene: Rv0078, LH57_00450 / Details (production host): CLONAGE SITES: NdeI-BamH1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold pLysS AG / References: UniProt: O53623
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.07 Å3/Da / Density % sol: 40.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 200 mM NaCl, 200 mM Na Citrate pH 4.2 and 15%polyethylene glycol monomethylether 5000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98011 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 13, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 16231 / % possible obs: 99 % / Redundancy: 7 % / Biso Wilson estimate: 60.4 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.083 / Net I/σ(I): 1.45
Reflection shellResolution: 2.4→2.54 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.83 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 2440 / CC1/2: 0.88 / % possible all: 94.7

-
Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
XDSVERSION March 30, 2013data reduction
MOLREP11.0.15phasing
XDSVERSION Oct 15, 2015data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5N1C

5n1c


Resolution: 2.4→38.36 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.926 / SU B: 11.989 / SU ML: 0.262 / Cross valid method: THROUGHOUT / ESU R: 0.46 / ESU R Free: 0.283 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26845 809 5 %RANDOM
Rwork0.2192 ---
obs0.22166 15361 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 62.589 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0.03 Å2-0 Å2
3----0.03 Å2
Refinement stepCycle: 1 / Resolution: 2.4→38.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2864 0 0 4 2868
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0192903
X-RAY DIFFRACTIONr_bond_other_d0.0010.022890
X-RAY DIFFRACTIONr_angle_refined_deg1.5151.9653937
X-RAY DIFFRACTIONr_angle_other_deg0.97136573
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8455375
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.24922.344128
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.44615482
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2751538
X-RAY DIFFRACTIONr_chiral_restr0.0810.2460
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213317
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02661
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_it4.3725.8741509
X-RAY DIFFRACTIONr_mcbond_other4.3265.8731508
X-RAY DIFFRACTIONr_mcangle_it6.1328.81881
X-RAY DIFFRACTIONr_mcangle_other6.138.8031882
X-RAY DIFFRACTIONr_scbond_it5.5916.6241394
X-RAY DIFFRACTIONr_scbond_other5.5896.6261395
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.4489.6652057
X-RAY DIFFRACTIONr_long_range_B_refined10.12770.8313173
X-RAY DIFFRACTIONr_long_range_B_other10.12670.8543174
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 11044 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.1 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 58 -
Rwork0.344 1097 -
obs--99.48 %

+
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