[English] 日本語
Yorodumi
- PDB-1p4s: Solution structure of Mycobacterium tuberculosis adenylate kinase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1p4s
TitleSolution structure of Mycobacterium tuberculosis adenylate kinase
ComponentsAdenylate kinase
KeywordsTRANSFERASE / alpha/beta
Function / homology
Function and homology information


nucleoside triphosphate metabolic process / nucleoside monophosphate metabolic process / CDP biosynthetic process / nucleoside diphosphate metabolic process / (d)CMP kinase activity / UMP kinase activity / adenylate kinase / adenylate kinase activity / AMP salvage / UDP biosynthetic process ...nucleoside triphosphate metabolic process / nucleoside monophosphate metabolic process / CDP biosynthetic process / nucleoside diphosphate metabolic process / (d)CMP kinase activity / UMP kinase activity / adenylate kinase / adenylate kinase activity / AMP salvage / UDP biosynthetic process / nucleoside diphosphate kinase activity / purine nucleobase metabolic process / peptidoglycan-based cell wall / phosphorylation / ATP binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Adenylate kinase / Adenylate kinase, conserved site / Adenylate kinase signature. / Adenylate kinase/UMP-CMP kinase / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Adenylate kinase / Adenylate kinase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodSOLUTION NMR / simulated annealing protocol
AuthorsMiron, S. / Munier-Lehmann, H. / Craescu, C.T.
CitationJournal: Biochemistry / Year: 2004
Title: Structural and Dynamic Studies on Ligand-Free Adenylate Kinase from Mycobacterium tuberculosis Revealed a Closed Conformation that Can Be Related to the Reduced Catalytic Activity.
Authors: Miron, S. / Munier-Lehmann, H. / Craescu, C.T.
History
DepositionApr 24, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 20, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Adenylate kinase


Theoretical massNumber of molelcules
Total (without water)20,1531
Polymers20,1531
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest restraint violations and lowest energy
RepresentativeModel #12closest to the average

-
Components

#1: Protein Adenylate kinase / ATP-AMP transphosphorylase


Mass: 20152.910 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: ADK OR RV0733 OR MT0757 OR MTV041.07 / Plasmid: pet22b / Production host: Escherichia coli (E. coli) / Strain (production host): Bli5/pHL20
References: UniProt: P69440, UniProt: P9WKF5*PLUS, adenylate kinase

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1122D NOESY, TOCSY, COSY
1232D NOESY, TOCSY, COSY
1343D 15N NOESY-HSQC, TOCSY-HSQC
1413D 15N, 13C HNCA, HN(CO)CA, HN(CA)CB, HN(CO)CACB, (H)CCH-TOCSY

-
Sample preparation

Details
Solution-IDContentsSolvent system
11.2 mM adenylate kinase 15N, 13C, 50mM potassium phosphate buffer pH 7.195% H20, 5% D2O,
21.0 mM adenylate kinase 50mM potassium phosphate buffer pH 7.1100% D2O
31.2 mM adenylate kinase 50mM potassium phosphate buffer pH 7.195% H20, 5% D2O,
41.2 mM adenylate kinase 15N, 50mM potassium phosphate buffer pH 7.195% H20, 5% D2O,
Sample conditionspH: 7.1 / Temperature: 308 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian UNITYVarianUNITY5001
Varian INOVAVarianINOVA7502

-
Processing

NMR softwareName: Insight II / Developer: MSI / Classification: refinement
RefinementMethod: simulated annealing protocol / Software ordinal: 1
Details: the structures are based on a 1809 are NOE-derived distance constraints, 191 dihedral angle restraints,159 distance restraints from hydrogen bonds.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest restraint violations and lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

+
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://pdbjlvh1.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