[English] 日本語
Yorodumi
- PDB-5d1w: Crystal structure of Mycobacterium tuberculosis Rv3249c transcrip... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5d1w
TitleCrystal structure of Mycobacterium tuberculosis Rv3249c transcriptional regulator.
ComponentsRv3249c transcriptional regulator
KeywordsTRANSCRIPTION / Mycobacterium tuberculosis / transcriptional regulator
Function / homologyTetracyclin repressor C-terminal, Actinobacteria / Bacterial Tetracyclin repressor, C-terminal domain / Bacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type / TetR-type HTH domain profile. / Homeobox-like domain superfamily / DNA binding / PALMITIC ACID / Possible transcriptional regulatory protein (Probably TetR-family)
Function and homology information
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 3.59 Å
AuthorsChou, T.-H. / Delmar, J. / Su, C.-C. / Yu, E.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Structural Basis for the Regulation of the MmpL Transporters of Mycobacterium tuberculosis.
Authors: Delmar, J.A. / Chou, T.H. / Wright, C.C. / Licon, M.H. / Doh, J.K. / Radhakrishnan, A. / Kumar, N. / Lei, H.T. / Bolla, J.R. / Rajashankar, K.R. / Su, C.C. / Purdy, G.E. / Yu, E.W.
History
DepositionAug 4, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 7, 2015Group: Database references
Revision 1.2Dec 2, 2015Group: Database references
Revision 1.3Nov 22, 2017Group: Database references / Derived calculations / Refinement description
Category: citation / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Rv3249c transcriptional regulator
B: Rv3249c transcriptional regulator
C: Rv3249c transcriptional regulator
D: Rv3249c transcriptional regulator
E: Rv3249c transcriptional regulator
F: Rv3249c transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,93010
Polymers141,9056
Non-polymers1,0264
Water0
1
A: Rv3249c transcriptional regulator
B: Rv3249c transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8144
Polymers47,3022
Non-polymers5132
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4900 Å2
ΔGint-17 kcal/mol
Surface area17670 Å2
MethodPISA
2
C: Rv3249c transcriptional regulator
D: Rv3249c transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8144
Polymers47,3022
Non-polymers5132
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5020 Å2
ΔGint-16 kcal/mol
Surface area17250 Å2
MethodPISA
3
E: Rv3249c transcriptional regulator
F: Rv3249c transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)47,3022
Polymers47,3022
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3080 Å2
ΔGint-17 kcal/mol
Surface area17970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)234.048, 75.493, 125.361
Angle α, β, γ (deg.)90.000, 121.550, 90.000
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein
Rv3249c transcriptional regulator


Mass: 23650.770 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: Rv3249c, LH57_17765 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: O05892
#2: Chemical
ChemComp-PLM / PALMITIC ACID / Palmitic acid


Mass: 256.424 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H32O2

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.33 Å3/Da / Density % sol: 63.01 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.2 / Details: Imidazole, HEPES, sodium chloride

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 2, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.59→40 Å / Num. obs: 21152 / % possible obs: 95.7 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.07 / Rrim(I) all: 0.134 / Χ2: 1.015 / Net I/av σ(I): 11 / Net I/σ(I): 6.9 / Num. measured all: 74518
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.59-3.723.60.39121260.9160.2380.4581.02997.6
3.72-3.873.60.32121250.9710.1980.3781.03897.7
3.87-4.043.50.2321450.9760.1420.271.02697.1
4.04-4.263.50.17621020.9760.1080.2071.02396.1
4.26-4.523.40.14220320.9830.0880.1671.00192.7
4.52-4.873.50.12820950.9760.0780.151.02595.4
4.87-5.363.60.11921600.9870.0720.1391.00697.3
5.36-6.133.50.11921210.9840.0730.140.99496.2
6.13-7.723.50.08620590.990.0530.1011.00291.7
7.72-403.40.07421870.990.0450.0871.00695.3

-
Processing

Software
NameVersionClassification
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.15data extraction
SHELXphasing
Cootmodel building
RefinementMethod to determine structure: SIRAS / Resolution: 3.59→39.631 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 33.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2782 1077 5.11 %
Rwork0.177 --
obs0.182 21071 95.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 150.87 Å2 / Biso mean: 56.693 Å2 / Biso min: 9.09 Å2
Refinement stepCycle: final / Resolution: 3.59→39.631 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8912 0 196 0 9108
Biso mean--29.29 --
Num. residues----1162

+
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