[English] 日本語
Yorodumi
- PDB-6yj2: Structural and DNA binding studies of the transcriptional repress... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6yj2
TitleStructural and DNA binding studies of the transcriptional repressor Rv2506 (BkaR) from Mycobacterium tuberculosis supports a role in L-Leucine catabolism
ComponentsProbable transcriptional regulatory protein (Probably TetR-family)
KeywordsDNA BINDING PROTEIN / Tuberculosis / Branch-chain amino acid catabolism / TetR Family
Function / homology
Function and homology information


symbiont-mediated evasion of host immune response / transcription cis-regulatory region binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription / identical protein binding
Similarity search - Function
HTH-type transcriptional repressor KstR2, C-terminal / 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 (Probably TetR-family)
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKeep, N.H. / Pritchard, J.E. / Sula, A. / Cole, A.R. / Kendall, S.L.
CitationJournal: To be published
Title: Structural and DNA binding studies of the transcriptional repressor Rv2506 (BkaR) from Mycobacterium tuberculosis supports a role in L-Leucine catabolism
Authors: Pritchard, J.E. / Sula, A. / Cole, A.R. / Kendall, S.L. / Keep, N.H.
History
DepositionApr 2, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 14, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Probable transcriptional regulatory protein (Probably TetR-family)
D: Probable transcriptional regulatory protein (Probably TetR-family)
A: Probable transcriptional regulatory protein (Probably TetR-family)
C: Probable transcriptional regulatory protein (Probably TetR-family)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,75212
Polymers93,0154
Non-polymers7378
Water4,396244
1
B: Probable transcriptional regulatory protein (Probably TetR-family)
A: Probable transcriptional regulatory protein (Probably TetR-family)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,8766
Polymers46,5072
Non-polymers3684
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3820 Å2
ΔGint-30 kcal/mol
Surface area17670 Å2
MethodPISA
2
D: Probable transcriptional regulatory protein (Probably TetR-family)
C: Probable transcriptional regulatory protein (Probably TetR-family)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,8766
Polymers46,5072
Non-polymers3684
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3720 Å2
ΔGint-25 kcal/mol
Surface area17660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)181.764, 52.874, 91.919
Angle α, β, γ (deg.)90.000, 90.100, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21D
12B
22A
13B
23C
14D
24A
15D
25C
16A
26C

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERLEULEUBA24 - 21524 - 215
21SERSERLEULEUDB24 - 21524 - 215
12ASPASPCYSCYSBA25 - 21425 - 214
22ASPASPCYSCYSAC25 - 21425 - 214
13PHEPHECYSCYSBA28 - 21428 - 214
23PHEPHECYSCYSCD28 - 21428 - 214
14ASPASPCYSCYSDB25 - 21425 - 214
24ASPASPCYSCYSAC25 - 21425 - 214
15PHEPHECYSCYSDB28 - 21428 - 214
25PHEPHECYSCYSCD28 - 21428 - 214
16PHEPHEARGARGAC28 - 21328 - 213
26PHEPHEARGARGCD28 - 21328 - 213

NCS ensembles :
ID
1
2
3
4
5
6

-
Components

#1: Protein
Probable transcriptional regulatory protein (Probably TetR-family)


Mass: 23253.721 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: Rv2506 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O06169
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 244 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.37 Å3/Da / Density % sol: 48.2 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.22 M ammonium citrate tribasic pH 7.0, 26.4 % (w/v) polyethylene glycol (PEG) 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 7, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2→46 Å / Num. obs: 59229 / % possible obs: 99.7 % / Redundancy: 3.4 % / Biso Wilson estimate: 32.6 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.034 / Net I/σ(I): 12.5
Reflection shellResolution: 2→2.05 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.554 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 4355 / CC1/2: 0.808 / Rpim(I) all: 0.351 / % possible all: 99.8

-
Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4G12

4g12


Resolution: 2→46 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.946 / SU B: 4.343 / SU ML: 0.118 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.17 / ESU R Free: 0.15
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2245 2946 5 %RANDOM
Rwork0.192 ---
obs0.1936 56283 99.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 189.62 Å2 / Biso mean: 51.997 Å2 / Biso min: 21.31 Å2
Baniso -1Baniso -2Baniso -3
1-0.51 Å2-0 Å2-0.14 Å2
2---2.19 Å20 Å2
3---1.67 Å2
Refinement stepCycle: final / Resolution: 2→46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5752 0 48 244 6044
Biso mean--61.09 49 -
Num. residues----755
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0135874
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175828
X-RAY DIFFRACTIONr_angle_refined_deg1.4741.6317936
X-RAY DIFFRACTIONr_angle_other_deg1.3391.57513295
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5155749
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.86418.805343
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.48815970
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1811581
X-RAY DIFFRACTIONr_chiral_restr0.0760.2751
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026681
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021366
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11B58070.09
12D58070.09
21B56690.09
22A56690.09
31B54590.1
32C54590.1
41D56060.1
42A56060.1
51D55210.09
52C55210.09
61A54590.09
62C54590.09
LS refinement shellResolution: 2→2.052 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 221 -
Rwork0.277 4123 -
all-4344 -
obs--99.68 %

+
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