[English] 日本語
Yorodumi
- PDB-3kx0: Crystal Structure of the PAS domain of Rv1364c -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3kx0
TitleCrystal Structure of the PAS domain of Rv1364c
ComponentsUncharacterized protein Rv1364c/MT1410
KeywordsSIGNALING PROTEIN / PAS domain / Rv1364c / Sensory domain / Mycobacteium tuberculosis / Small molecule binding domain
Function / homology
Function and homology information


alkaline phosphatase activity / protein serine/threonine phosphatase activity / myosin phosphatase activity / protein-serine/threonine phosphatase / phosphatase activity / protein serine/threonine/tyrosine kinase activity / manganese ion binding / non-specific serine/threonine protein kinase / protein serine kinase activity / protein serine/threonine kinase activity ...alkaline phosphatase activity / protein serine/threonine phosphatase activity / myosin phosphatase activity / protein-serine/threonine phosphatase / phosphatase activity / protein serine/threonine/tyrosine kinase activity / manganese ion binding / non-specific serine/threonine protein kinase / protein serine kinase activity / protein serine/threonine kinase activity / regulation of DNA-templated transcription / magnesium ion binding / ATP binding / identical protein binding
Similarity search - Function
Histidine kinase-like ATPase domain / : / Stage II sporulation protein E (SpoIIE) / PAS fold-4 / STAS domain / PAS fold / Sigma factor PP2C-like phosphatases / STAS domain / PPM-type phosphatase domain profile. / PPM-type phosphatase-like domain ...Histidine kinase-like ATPase domain / : / Stage II sporulation protein E (SpoIIE) / PAS fold-4 / STAS domain / PAS fold / Sigma factor PP2C-like phosphatases / STAS domain / PPM-type phosphatase domain profile. / PPM-type phosphatase-like domain / PPM-type phosphatase-like domain superfamily / STAS domain profile. / STAS domain / STAS domain superfamily / PAS-associated, C-terminal / PAC domain profile. / PAS domain / Beta-Lactamase / PAS domain / PAS domain superfamily / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ISOPROPYL ALCOHOL / Multidomain regulatory protein Rv1364c / Multidomain regulatory protein Rv1364c
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsJaiswal, R.K. / Gopal, B.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2010
Title: Role of a PAS sensor domain in the Mycobacterium tuberculosis transcription regulator Rv1364c
Authors: Jaiswal, R.K. / Manjeera, G. / Gopal, B.
History
DepositionDec 2, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
X: Uncharacterized protein Rv1364c/MT1410
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1702
Polymers21,1101
Non-polymers601
Water905
1
X: Uncharacterized protein Rv1364c/MT1410
hetero molecules

X: Uncharacterized protein Rv1364c/MT1410
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,3394
Polymers42,2192
Non-polymers1202
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_455-x-1,-y,z1
Buried area3890 Å2
ΔGint-21 kcal/mol
Surface area13280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.609, 59.609, 173.327
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222

-
Components

#1: Protein Uncharacterized protein Rv1364c/MT1410


Mass: 21109.510 Da / Num. of mol.: 1 / Fragment: UNP residues 1-163
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: Rv1364c / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 / References: UniProt: Q11034, UniProt: P9WLZ7*PLUS
#2: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / 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: 2.11 Å3/Da / Density % sol: 41.58 %
Crystal growTemperature: 300 K / Method: under oil / pH: 8
Details: 2.5M ammonium sulphate, 5% Isopropanol, .1M tris-chloride, pH 8, Under oil, temperature 300K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.95373 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 24, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 2.3→57.74 Å / Num. obs: 8811 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 17 % / Biso Wilson estimate: 39.6 Å2 / Rmerge(I) obs: 0.097 / Rsym value: 0.1 / Net I/σ(I): 21.2
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 17.7 % / Rmerge(I) obs: 0.573 / Mean I/σ(I) obs: 5.2 / Num. unique all: 21601 / Rsym value: 0.59 / % possible all: 100

-
Processing

Software
NameVersionClassification
SOLVEphasing
PHENIX(phenix.refine: 1.5_2)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.3→49.475 Å / SU ML: 0.38 / σ(F): 0.02 / σ(I): 2 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2744 399 4.72 %RANDOM
Rwork0.2329 ---
obs0.2349 8445 96.42 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.471 Å2 / ksol: 0.36 e/Å3
Displacement parametersBiso mean: 57.628 Å2
Baniso -1Baniso -2Baniso -3
1-8.784 Å2-0 Å2-0 Å2
2--8.784 Å20 Å2
3----17.568 Å2
Refine analyzeLuzzati coordinate error obs: 0.38 Å
Refinement stepCycle: LAST / Resolution: 2.3→49.475 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms994 0 4 5 1003
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071031
X-RAY DIFFRACTIONf_angle_d1.0781401
X-RAY DIFFRACTIONf_dihedral_angle_d20.273372
X-RAY DIFFRACTIONf_chiral_restr0.076148
X-RAY DIFFRACTIONf_plane_restr0.004191
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3001-2.63290.32521230.23362482X-RAY DIFFRACTION93
2.6329-3.3170.24211350.22822659X-RAY DIFFRACTION97
3.317-49.48660.26821410.2312905X-RAY DIFFRACTION99
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)
10.78590.5288-0.10180.830.04922.61020.1475-0.2030.1090.25590.23360.022-0.29980.1262-0.21180.43860.10780.02610.1334-0.00870.2998-28.53373.326722.8689
26.4253-2.1773-1.6574.92223.45592.40390.48021.15671.2559-1.5301-0.2674-0.4476-1.63980.3037-0.16290.4862-0.29870.1010.3813-0.12140.5495-18.472715.710815.798
34.93630.6137-3.44890.43471.05576.79520.65080.8331.0298-0.9028-0.026-0.8789-1.9395-0.1923-0.61430.7570.01110.11960.25380.07140.3976-27.5215.36077.9303
42.2265-0.9297-0.9720.29841.20051.50750.16980.45780.3541-0.09320.1802-0.1794-0.6396-0.3988-0.21070.45110.0130.07560.22520.01190.2593-28.4529.05689.4304
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain X and resid 4:47)X4 - 47
2X-RAY DIFFRACTION2(chain X and resid 48:74)X48 - 74
3X-RAY DIFFRACTION3(chain X and resid 75:104)X75 - 104
4X-RAY DIFFRACTION4(chain X and resid 105:138)X105 - 138

+
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