[English] 日本語
Yorodumi
- PDB-1te4: Solution structure of MTH187. Ontario Centre for Structural Prote... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1te4
TitleSolution structure of MTH187. Ontario Centre for Structural Proteomics target MTH0187_1_111; Northeast Structural Genomics Target TT740
Componentsconserved protein MTH187
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / MTH187 / Methanobacterium thermoautotrophicum / structural proteomics / HEAT-like repeat / OCSP / NESG / PROTEIN STRUCTURE INITIATIVE / PSI / Northeast Structural Genomics Consortium
Function / homologyPBS lyase HEAT-like repeat / E-Z type HEAT repeats / PBS lyase HEAT-like repeat / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha / Conserved protein
Function and homology information
Biological speciesMethanothermobacter thermautotrophicus (archaea)
MethodSOLUTION NMR / simulated annealing
AuthorsGignac, I. / Julien, O. / Yee, A. / Arrowsmith, C.H. / Gagne, S.M. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: J.Biomol.Nmr / Year: 2006
Title: MTH187 from Methanobacterium thermoautotrophicum has three HEAT-like Repeats.
Authors: Julien, O. / Gignac, I. / Hutton, A. / Yee, A. / Arrowsmith, C.H. / Gagne, S.M.
History
DepositionMay 24, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 13, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_database_related ...database_2 / pdbx_database_related / 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_database_related.db_name / _struct_ref_seq_dif.details
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: conserved protein MTH187


Theoretical massNumber of molelcules
Total (without water)14,5821
Polymers14,5821
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)40 / 100structures with the lowest energy
RepresentativeModel #1closest to the average

-
Components

#1: Protein conserved protein MTH187


Mass: 14582.253 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanothermobacter thermautotrophicus (archaea)
Description: The protein was purified on a Nickel column. / Gene: mt0187 / Plasmid: pET-15b / Production host: Escherichia coli (E. coli) / References: UniProt: O26289

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
11115N-TOCSY-HSQC
12115N-NOESY-HSQC
132CBCA(CO)NH
142HN(CA)CB
152HNCO
162(H)CCH-TOCSY
172HN(CA)CO
182HCA(CO)N
192HN(CO)CA
1102CC(CO)NH
1112HCACO
NMR detailsText: 15N-TOCSY-HSQC acquired at 500MHz, mix=100ms; 15N-NOESY-HSQC acquired at 800MHz, mix=100ms; others acquired at 600MHz

-
Sample preparation

Details
Solution-IDContentsSolvent system
10.47 mM MTH187 U-15N, 25 mM potassium phosphate, 22 mM CHAPS, 10 mM NaCl, 0.5 mM DSS, 90% H2O, 10% D2O90% H2O/10% D2O
20.47 mM MTH187 U-15N,13c, 25 mM potassium phosphate, 22 mM CHAPS, 10 mM NaCl, 0.5 mM DSS, 90% H2O, 10% D2O90% H2O/10% D2O
Sample conditionsIonic strength: 0.06 / pH: 6.2 / Pressure: 101.3 KPA / Temperature: 321.2 K

-
NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA5001
Varian INOVAVarianINOVA6002
Varian INOVAVarianINOVA8003

-
Processing

NMR software
NameVersionClassification
ARIA1.2structure solution
CNS1.1structure solution
CNS1.1refinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: the structures are based on a total of 2546 constraints: 2363 NOE-derived distance restraints, 47 from coupling constants, 127 dihedral angle restraints and 9 distance restraints from hydrogen bonds
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 40

+
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