[English] 日本語
Yorodumi
- PDB-2ko1: Solution NMR structure of the ACT domain from GTP pyrophosphokina... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2ko1
TitleSolution NMR structure of the ACT domain from GTP pyrophosphokinase of Chlorobium tepidum. Northeast Structural Genomics Consortium Target CtR148A
ComponentsGTP pyrophosphokinase
KeywordsTRANSFERASE / homodimer / alpha+beta / Kinase / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


guanosine tetraphosphate metabolic process / GTP diphosphokinase activity / GTP diphosphokinase / RNA binding
Similarity search - Function
RelA/SpoT, AH and RIS domains / RelA/SpoT, AH and RIS domains / HD domain / RelA/SpoT family / RelA/SpoT, TGS domain / ACT domain / Region found in RelA / SpoT proteins / RelA/SpoT / Region found in RelA / SpoT proteins / TGS domain ...RelA/SpoT, AH and RIS domains / RelA/SpoT, AH and RIS domains / HD domain / RelA/SpoT family / RelA/SpoT, TGS domain / ACT domain / Region found in RelA / SpoT proteins / RelA/SpoT / Region found in RelA / SpoT proteins / TGS domain / ACT domain / ACT domain profile. / ACT domain / ACT-like domain / TGS domain profile. / TGS / TGS-like / Beta-grasp domain superfamily / Metal dependent phosphohydrolases with conserved 'HD' motif. / HD/PDEase domain / Nucleotidyltransferase superfamily / S4 RNA-binding domain profile. / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
GTP pyrophosphokinase
Similarity search - Component
Biological speciesChlorobaculum tepidum (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsEletsky, A. / Garcia, E. / Wang, H. / Ciccosanti, C. / Jiang, M. / Nair, R. / Rost, B. / Acton, T.B. / Xiao, R. / Everett, J.K. ...Eletsky, A. / Garcia, E. / Wang, H. / Ciccosanti, C. / Jiang, M. / Nair, R. / Rost, B. / Acton, T.B. / Xiao, R. / Everett, J.K. / Lee, H. / Prestegard, J.H. / Montelione, G.T. / Szyperski, T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution NMR structure of the ACT domain from GTP pyrophosphokinase of Chlorobium tepidum
Authors: Eletsky, A. / Garcia, E. / Wang, H. / Ciccosanti, C. / Jiang, M. / Nair, R. / Rost, B. / Acton, T.B. / Xiao, R. / Everett, J.K. / Lee, H. / Prestegard, J. / Montelione, G.T. / Szyperski, T.
History
DepositionSep 8, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 29, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / 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 / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: GTP pyrophosphokinase
B: GTP pyrophosphokinase


Theoretical massNumber of molelcules
Total (without water)20,1012
Polymers20,1012
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1lowest energy

-
Components

#1: Protein GTP pyrophosphokinase / CtR148A


Mass: 10050.672 Da / Num. of mol.: 2 / Mutation: I16N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlorobaculum tepidum (bacteria) / Strain: TLS / Gene: CT1545, relA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+ Magic / References: UniProt: Q8KC80, GTP diphosphokinase

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1111D 15N T1
1211D 15N T2
1312D 1H-15N HSQC
1412D 1H-13C HSQC aliphatic
1512D 1H-13C CT-HSQC aliphatic
1612D 1H-13C CT-HSQC aromatic
1713D CBCA(CO)NH
1813D HN(CA)CB
1913D HNCO
11013D HN(CA)CO
11113D HBHA(CO)NH
11213D (H)CCH-COSY
11313D (H)CCH-TOCSY
11413D 1H-13C NOESY
11513D 1H-15N/13C NOESY
11622D 1H-13C CT-HSQC methyl
11722D 1H-15N HSQC J-MODULATED
11842D 1H-15N HSQC J-MODULATED
11952D 1H-15N HSQC J-MODULATED
12033D 1H-13C X-filtered NOESY

-
Sample preparation

Details
Solution-IDContentsSolvent system
10.3 mM [U-100% 13C; U-100% 15N] CtR148A, 20 mM MES, 200 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 50 uM DSS, 0.05 % sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
20.5 mM [U-5% 13C; U-100% 15N] CtR148A, 20 mM MES, 200 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 50 uM DSS, 0.05 % sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
30.5 mM [U-100% 13C; U-100% 15N] CtR148A, 20 mM MES, 200 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 50 uM DSS, 0.05 % sodium azide, 0.5 mM CtR148A, 90% H2O/10% D2O90% H2O/10% D2O
40.3 mM [U-5% 13C; U-100% 15N] CtR148A, 18 mM MES, 180 mM sodium chloride, 4.5 mM calcium chloride, 9 mM DTT, 45 uM DSS, 0.045 % sodium azide, 4 % polyethylene glycol, 84% H2O/16% D2O84% H2O/16% D2O
50.45 mM [U-5% 13C; U-100% 15N] CtR148A, 18 mM MES, 180 mM sodium chloride, 4.5 mM calcium chloride, 9 mM DTT, 45 uM DSS, 0.045 % sodium azide, 7 % polyacrylamide, 86% H2O/14% D2O86% H2O/14% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.3 mMCtR148A-1[U-100% 13C; U-100% 15N]1
20 mMMES-21
200 mMsodium chloride-31
5 mMcalcium chloride-41
10 mMDTT-51
50 uMDSS-61
0.05 %sodium azide-71
0.5 mMCtR148A-8[U-5% 13C; U-100% 15N]2
20 mMMES-92
200 mMsodium chloride-102
5 mMcalcium chloride-112
10 mMDTT-122
50 uMDSS-132
0.05 %sodium azide-142
0.5 mMCtR148A-15[U-100% 13C; U-100% 15N]3
20 mMMES-163
200 mMsodium chloride-173
5 mMcalcium chloride-183
10 mMDTT-193
50 uMDSS-203
0.05 %sodium azide-213
0.5 mMCtR148A-223
0.3 mMCtR148A-23[U-5% 13C; U-100% 15N]4
18 mMMES-244
180 mMsodium chloride-254
4.5 mMcalcium chloride-264
9 mMDTT-274
45 uMDSS-284
0.045 %sodium azide-294
4 %polyethylene glycol-304
0.45 mMCtR148A-31[U-5% 13C; U-100% 15N]5
18 mMMES-325
180 mMsodium chloride-335
4.5 mMcalcium chloride-345
9 mMDTT-355
45 uMDSS-365
0.045 %sodium azide-375
7 %polyacrylamide-385
Sample conditionsIonic strength: 225 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA7501
Varian INOVAVarianINOVA6002
Varian INOVAVarianINOVA6003

-
Processing

NMR software
NameVersionDeveloperClassification
VnmrJ2.1BVariancollection
PROSA6.4Guntertprocessing
CARA1.8.4Keller and Wuthrichchemical shift assignment
CARA1.8.4Keller and Wuthrichdata analysis
CARA1.8.4Keller and Wuthrichpeak picking
PINE1Bahrami, Markley, Assadi, and Eghbalniachemical shift assignment
TALOS+1.2009.0721.18Yang,Cornilescu, Delaglio and Baxdata analysis
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
CNS1.2.1Brunger, Adams, Clore, Gros, Nilges and Readrefinement
AutoStructure2.2.1Huang, Tejero, Powers and Montelionestructure validation
PSVS1.3Bhattacharya and Montelionestructure validation
RefinementMethod: simulated annealing / Software ordinal: 1
Details: Structure determination was performed iteratively with CYANA v2.1 and CYANA v3.0 using NOE-based constraints, PHI and PSI dihedral angle constraints from TALOS, and RDCs from two alignment ...Details: Structure determination was performed iteratively with CYANA v2.1 and CYANA v3.0 using NOE-based constraints, PHI and PSI dihedral angle constraints from TALOS, and RDCs from two alignment media. The 20 conformers out of 100 with the lowest target function were further refined by simulated annealing in explicit water bath using the program CNS with PARAM19 force field.
NMR constraintsNOE constraints total: 5263 / NOE intraresidue total count: 888 / NOE long range total count: 2011 / NOE medium range total count: 1139 / NOE sequential total count: 1225 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 116 / Protein psi angle constraints total count: 116
NMR representativeSelection criteria: lowest energy
NMR ensembleAverage torsion angle constraint violation: 0.12 ° / Conformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20 / Maximum torsion angle constraint violation: 3.5 ° / Maximum upper distance constraint violation: 0.39 Å
NMR ensemble rmsDistance rms dev: 0.014 Å

+
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