[English] 日本語
Yorodumi
- PDB-4w1u: Crystal structure of Rv3557c/KstR2, a transcriptional repressor i... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4w1u
TitleCrystal structure of Rv3557c/KstR2, a transcriptional repressor involved in cholesterol metabolism in Mycobacterium tuberculosis
ComponentsHTH-type transcriptional repressor KstR2
KeywordsTRANSCRIPTION / TetR-family repressor / cholesterol
Function / homology
Function and homology information


transcription cis-regulatory region binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription / DNA binding
Similarity search - Function
HTH-type transcriptional repressor KstR2, C-terminal / Tetracyclin repressor-like, 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 ...HTH-type transcriptional repressor KstR2, C-terminal / Tetracyclin repressor-like, 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
HTH-type transcriptional repressor KstR2
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.875 Å
AuthorsDawes, S.S. / Kendall, S.K. / Baker, E.N. / Lott, J.S.
CitationJournal: To Be Published
Title: Crystal structure of Rv3557c/KstR2, a transcriptional repressor involved in cholesterol metabolism in Mycobacterium tuberculosis.
Authors: Dawes, S.S. / Kendall, S.K. / Baker, E.N. / Lott, J.S.
History
DepositionAug 13, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Derived calculations / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_struct_oper_list / software
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Sep 27, 2023Group: 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 repressor KstR2


Theoretical massNumber of molelcules
Total (without water)23,2501
Polymers23,2501
Non-polymers00
Water2,846158
1
A: HTH-type transcriptional repressor KstR2

A: HTH-type transcriptional repressor KstR2


Theoretical massNumber of molelcules
Total (without water)46,5012
Polymers46,5012
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_757-x+2,y,-z+21
Buried area3330 Å2
ΔGint-23 kcal/mol
Surface area17930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.356, 90.292, 49.693
Angle α, β, γ (deg.)90.000, 128.210, 90.000
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein HTH-type transcriptional repressor KstR2


Mass: 23250.281 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: ATCC 25618 / H37Rv / Gene: kstR2, Rv3557c / Plasmid: pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / Variant (production host): DE3 / References: UniProt: P9WMB9
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 158 / 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: 2.78 Å3/Da / Density % sol: 55.77 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.9 / Details: 0.2 M citric acid, 14% MPEG 5000

-
Data collection

DiffractionMean temperature: 203 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 11, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.86→48.113 Å / Num. all: 19815 / Num. obs: 19815 / % possible obs: 94.3 % / Redundancy: 6.3 % / Biso Wilson estimate: 24.67 Å2 / Rpim(I) all: 0.02 / Rrim(I) all: 0.05 / Rsym value: 0.046 / Net I/av σ(I): 13.013 / Net I/σ(I): 25.1 / Num. measured all: 124168
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
1.86-1.966.10.3924.41488224410.1710.3924.580
1.96-2.086.30.2443.11725027510.1050.2447.494.8
2.08-2.236.30.1515.11634826070.0650.15111.595.6
2.23-2.46.30.17.51529324330.0430.116.996.2
2.4-2.636.30.06910.81424622610.030.06922.296.8
2.63-2.946.30.047151286820410.020.0473097.5
2.94-3.46.30.03320.91163718420.0140.03340.298.2
3.4-4.166.30.02624984715590.0110.0265798.7
4.16-5.896.30.02324.1765912150.010.0236599.4
5.89-26.66.20.02521.941386650.0110.0256296.8

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.9 Å26.6 Å
Translation1.9 Å26.6 Å

-
Processing

Software
NameVersionClassification
iMOSFLMdata reduction
SCALA3.3.16data scaling
ARPmodel building
WARPmodel building
PDB_EXTRACT3.14data extraction
PHASERphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2IBD

2ibd


Resolution: 1.875→26.6 Å / FOM work R set: 0.8552 / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 21.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2002 1008 5.09 %
Rwork0.1716 18803 -
obs0.1731 19811 96.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 76.65 Å2 / Biso mean: 31.57 Å2 / Biso min: 11.4 Å2
Refinement stepCycle: final / Resolution: 1.875→26.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1541 0 0 158 1699
Biso mean---41.04 -
Num. residues----193
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071632
X-RAY DIFFRACTIONf_angle_d0.9262222
X-RAY DIFFRACTIONf_chiral_restr0.039238
X-RAY DIFFRACTIONf_plane_restr0.005294
X-RAY DIFFRACTIONf_dihedral_angle_d14.895608
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.875-1.97350.27751300.22832575270593
1.9735-2.09710.24181410.18412624276595
2.0971-2.2590.19211440.16852685282996
2.259-2.48620.22971380.17222697283596
2.4862-2.84550.2091530.18132685283897
2.8455-3.58370.19081390.16792768290798
3.5837-26.6030.17881630.16012769293298
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.4723-2.70867.47687.1839-3.88642.0166-0.1138-0.45910.19020.4309-0.04320.3491-0.327-0.33660.13430.40360.03420.12270.3468-0.06390.324149.4007-2.312254.7595
21.02720.93120.0887.06041.39830.85280.1058-0.16550.09870.4156-0.0438-0.2472-0.01080.0265-0.0640.1234-0.0196-0.02180.2123-0.00620.125155.6861-16.932646.8057
34.4184-0.383-0.91166.31551.82517.11860.2057-0.25490.21170.1867-0.16350.2028-0.19740.0714-0.08290.0524-0.008-0.02940.1654-0.00310.117543.3747-28.285642.9899
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 34 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 35 through 150 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 151 through 200 )A0

+
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