[English] 日本語
Yorodumi
- PDB-1z9v: Solution Structure of MTH0776 from Methanobacterium thermoautotro... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1z9v
TitleSolution Structure of MTH0776 from Methanobacterium thermoautotrophicum (strain H)
Componentsconserved hypothetical protein MTH0776
KeywordsUNKNOWN FUNCTION / Solution Structure / Archaeabacterium
Function / homologyMTH0776-like / Domain of unknown function (DUF1894) / : / Conserved protein
Function and homology information
Biological speciesMethanothermobacter thermautotrophicus (archaea)
MethodSOLUTION NMR / simulated annealing protocol in XPLOR-NIH
AuthorsAmegbey, G. / Stothard, P. / Iakounine, A. / Yee, A. / Arrowsmith, C.H. / Wishart, D.S.
CitationJournal: J.Biomol.Nmr / Year: 2005
Title: Solution Structure of MTH0776 from Methanobacterium Thermoautotrophicum.
Authors: Amegbey, G. / Stothard, P. / Kuznetsova, E. / Yee, A. / Arrowsmith, C.H. / Wishart, D.S.
History
DepositionApr 4, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 22, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: conserved hypothetical protein MTH0776


Theoretical massNumber of molelcules
Total (without water)13,5841
Polymers13,5841
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 / 60structures with the least restraint violations
RepresentativeModel #1closest to the average

-
Components

#1: Protein conserved hypothetical protein MTH0776


Mass: 13583.732 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanothermobacter thermautotrophicus (archaea)
Strain: Delta H / Gene: MTH776 / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: GenBank: 2621867, UniProt: O26870*PLUS

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D HN(CA)CB, HNCA, CBCA(CO)NH, HNCO, H(CCO)NH, C(CO)NH, 15N-separated NOESY
222D2O-exchange 15N HSQC, 13C-separated NOESY, (H)CCH-TOCSY
333HNHA
4442D NOESY
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy.

-
Sample preparation

Details
Solution-IDContentsSolvent system
11mM MTH0776 U-15N,13C; 50mM NaH2PO4 buffer pH6.8, 300mM NaCl, 0.1mM DSS, 15mM DTT, 0.06% NaN3, 90% H2O, 10% D2O90% H2O/10% D2O
21mM MTH0776 U-15N,13C; 50mM NaH2PO4 buffer pH6.8, 300mM NaCl, 0.1mM DSS, 15mM DTT, 0.06% NaN3, 100% D2O100% D20
31mM MTH0776 U-15N; 50mM NaH2PO4 buffer pH6.8, 300mM NaCl, 0.1mM DSS, 15mM DTT, 0.06% NaN3, 90% H2O, 10% D2O90% H2O/10% D2O
41mM MTH0776 unlabelled; 50mM NaH2PO4 buffer pH6.8, 300mM NaCl, 0.1mM DSS, 15mM DTT, 0.06% NaN3, 90% H2O, 10% D2O90% H2O/10% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1300mM NaCl, 50mM NaH2PO4 6.8 ambient 298 K
2300mM NaCl, 50mM NaH2PO4 6.8 ambient 298 K
3300mM NaCl, 50mM NaH2PO4 6.8 ambient 298 K
4300mM NaCl, 50mM NaH2PO4 6.8 ambient 298 K

-
NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA5001
Varian INOVAVarianINOVA8002

-
Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1Ccollection
NMRPipeDelaglio, F., Grzesiek, S., Vuister, G., Zhu, G., Pfeifer, J. and Bax, A.processing
XPLOR-NIH2.9.6refinement
RefinementMethod: simulated annealing protocol in XPLOR-NIH / Software ordinal: 1
Details: The structures are based on a total of 2048 restraints, 1844 are NOE-derived distance constraints, 164 dihedral angle restraints, 40 distance restraints from hydrogen bonds.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 60 / 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