[English] 日本語
Yorodumi
- PDB-3ouv: SeMet Derivative of L512M mutant of PASTA domain 3 of Mycobacteri... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3ouv
TitleSeMet Derivative of L512M mutant of PASTA domain 3 of Mycobacterium tuberculosis PknB
ComponentsSerine/threonine protein kinaseSerine/threonine-specific protein kinase
KeywordsTRANSFERASE / Protein-Ligand interaction
Function / homology
Function and homology information


regulation of cellular biosynthetic process / regulation of primary metabolic process / non-specific serine/threonine protein kinase / phosphorylation / protein serine/threonine kinase activity / ATP binding / plasma membrane
Similarity search - Function
Trypsin Inhibitor V; Chain A - #20 / PASTA domain / PASTA domain / PASTA domain profile. / PASTA / Trypsin Inhibitor V; Chain A / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain ...Trypsin Inhibitor V; Chain A - #20 / PASTA domain / PASTA domain / PASTA domain profile. / PASTA / Trypsin Inhibitor V; Chain A / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Serine/threonine-protein kinase PknB
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Ra (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.004 Å
AuthorsPrigozhin, D.M. / Chen, T.Y. / Alber, T.
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Structural and Genetic Analyses of the Mycobacterium tuberculosis Protein Kinase B Sensor Domain Identify a Potential Ligand-binding Site.
Authors: Prigozhin, D.M. / Papavinasasundaram, K.G. / Baer, C.E. / Murphy, K.C. / Moskaleva, A. / Chen, T.Y. / Alber, T. / Sassetti, C.M.
History
DepositionSep 15, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 14, 2016Group: Database references
Revision 1.2Dec 14, 2016Group: Database references

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Serine/threonine protein kinase


Theoretical massNumber of molelcules
Total (without water)7,3221
Polymers7,3221
Non-polymers00
Water91951
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)24.439, 73.413, 32.583
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein Serine/threonine protein kinase / Serine/threonine-specific protein kinase


Mass: 7321.954 Da / Num. of mol.: 1 / Fragment: Extracellular Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Ra (bacteria)
Strain: H37Rv / Gene: pknB, MRA_0016 / Production host: Escherichia coli (E. coli) / References: UniProt: A5TY84
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 51 / 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 Å3/Da / Density % sol: 38.38 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 0.2 Lithium sulfate, 0.1 M Sodium acetate, 30% (v/v) MPD, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

-
Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1271 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 8, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1271 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 3995

-
Processing

SoftwareName: PHENIX / Version: (phenix.refine: dev_243) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.004→32.583 Å / SU ML: 0.23 / σ(F): 0.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2261 411 10.29 %
Rwork0.1763 --
obs0.1814 3995 93.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 61.42 Å2 / ksol: 0.454 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.9821 Å20 Å2-0 Å2
2--3.5727 Å20 Å2
3----1.4322 Å2
Refinement stepCycle: LAST / Resolution: 2.004→32.583 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms484 0 0 51 535
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007493
X-RAY DIFFRACTIONf_angle_d1.08675
X-RAY DIFFRACTIONf_dihedral_angle_d16.289180
X-RAY DIFFRACTIONf_chiral_restr0.06481
X-RAY DIFFRACTIONf_plane_restr0.00591
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0043-2.29430.25841290.19341081X-RAY DIFFRACTION88
2.2943-2.89030.21341360.16921193X-RAY DIFFRACTION94
2.8903-32.58730.21861460.17251310X-RAY DIFFRACTION98

+
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