[English] 日本語
Yorodumi
- PDB-2kwa: 1H, 13C and 15N backbone and side chain resonance assignments of ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2kwa
Title1H, 13C and 15N backbone and side chain resonance assignments of the N-terminal domain of the histidine kinase inhibitor KipI from Bacillus subtilis
ComponentsKinase A inhibitor
KeywordsTRANSFERASE INHIBITOR / Bacterial signal transduction / KipI / histidine kinase inhibition / Bacillus subtilis
Function / homology
Function and homology information


5-oxoprolinase (ATP-hydrolysing) / 5-oxoprolinase (ATP-hydrolyzing) activity / sporulation resulting in formation of a cellular spore / protein kinase inhibitor activity / ATP binding
Similarity search - Function
KipI family / Carboxyltransferase domain, subdomain C and D / Carboxyltransferase domain, subdomain C and D / Allophanate hydrolase subunit 1 / Gyrase A; domain 2 - #40 / Cyclophilin-like domain superfamily / Gyrase A; domain 2 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
5-oxoprolinase subunit B
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodSOLUTION NMR / molecular dynamics, simulated annealing
Model detailslowest energy, model 1
AuthorsHynson, R.M.G. / Kwan, A. / Jacques, D.A. / Mackay, J.P. / Trewhella, J.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: A Novel Structure of an Antikinase and its Inhibitor
Authors: Jacques, D.A. / Langley, D.B. / Hynson, R.M.G. / Whitten, A.E. / Kwan, A. / Guss, J.M. / Trewhella, J.
History
DepositionMar 31, 2010Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Nov 24, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Kinase A inhibitor


Theoretical massNumber of molelcules
Total (without water)11,5661
Polymers11,5661
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 500structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein Kinase A inhibitor / KipI-N / Sporulation inhibitor kipI


Mass: 11565.928 Da / Num. of mol.: 1 / Fragment: N-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: kipI / Production host: Escherichia coli (E. coli) / References: UniProt: P60495

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HN(CA)CB
1313D CBCA(CO)NH
1413D HNCO
1513D HN(CO)CA
1613D HNCA
1713D HN(CA)CO
1812D 1H-13C HSQC
1913D HBHA(CO)NH
11013D CC(CO)NH TOCSY
11113D 1H-15N TOCSY
11213D (H)CCH-TOCSY
11312D 1H-1H NOESY
11412D 1H-1H COSY
11513D 1H-1H TOCSY
1161HBCBCGCEHE
1171(HB)CB(CGCD)HD
11813D 1H-15N NOESY
11913D 1H-13C NOESY

-
Sample preparation

DetailsContents: 1mM [U-100% 15N] KipI-N-1, 1mM [U-100% 13C; U-100% 15N] KipI-N-2, 1mM KipI-N-3, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMKipI-N-1[U-100% 15N]1
1 mMKipI-N-2[U-100% 13C; U-100% 15N]1
1 mMKipI-N-31
Sample conditionsIonic strength: 0.2 / pH: 6.2 / Pressure: ambient / Temperature: 298 K

-
NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
TopSpin2.1-2.5Bruker Biospindata analysis
TopSpin2.1-2.5Bruker Biospincollection
SparkyGoddarddata analysis
SparkyGoddardchemical shift assignment
ARIALinge, O'Donoghue and Nilgeschemical shift assignment
ARIALinge, O'Donoghue and Nilgesstructure solution
ARIALinge, O'Donoghue and Nilgesrefinement
RefinementMethod: molecular dynamics, simulated annealing / Software ordinal: 1
Details: Heating and cooling steps changed from 10000, 5000 & 4000 to 20000, 20000 & 16000
NMR constraintsProtein phi angle constraints total count: 68 / Protein psi angle constraints total count: 68
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 500 / Conformers submitted total number: 20 / Maximum torsion angle constraint violation: 0 ° / Representative conformer: 1 / Torsion angle constraint violation method: ARIA 2.1

+
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