[English] 日本語
Yorodumi
- PDB-1tvi: Solution structure of TM1509 from Thermotoga maritima: VT1, a NES... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1tvi
TitleSolution structure of TM1509 from Thermotoga maritima: VT1, a NESGC target protein
ComponentsHypothetical UPF0054 protein TM1509
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / alpha + beta / mixed 4-stranded beta sheet / four helix bundle / Protein Structure Initiative / NESGC / PSI / Northeast Structural Genomics Consortium
Function / homology
Function and homology information


RNA endonuclease activity / metalloendopeptidase activity / rRNA processing / Hydrolases; Acting on ester bonds / zinc ion binding / cytoplasm
Similarity search - Function
Metalloproteases ("zincins"), catalytic domain / Endoribonuclease YbeY, conserved site / Uncharacterized protein family UPF0054 signature. / Endoribonuclease YbeY / Metalloprotease catalytic domain superfamily, predicted / Endoribonuclease YbeY / Collagenase (Catalytic Domain) / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Endoribonuclease YbeY
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodSOLUTION NMR / DYANA 1.5 with 30,000 TAD steps, simulated annealing
AuthorsPenhoat, C.H. / Atreya, H.S. / Kim, S. / Li, Z. / Yee, A. / Xiao, R. / Murray, D. / Arrowsmith, C.H. / Szyperski, T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: J.STRUCT.FUNCT.GENOM. / Year: 2005
Title: NMR solution structure of Thermotoga maritima protein TM1509 reveals a Zn-metalloprotease-like tertiary structure.
Authors: Penhoat, C.H. / Li, Z. / Atreya, H.S. / Kim, S. / Yee, A. / Xiao, R. / Murray, D. / Arrowsmith, C.H. / Szyperski, T.
History
DepositionJun 29, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 4, 2005Provider: 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_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / 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: Hypothetical UPF0054 protein TM1509


Theoretical massNumber of molelcules
Total (without water)20,1581
Polymers20,1581
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 / 100target function
RepresentativeModel #1lowest target function

-
Components

#1: Protein Hypothetical UPF0054 protein TM1509


Mass: 20157.539 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM1509 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9X1J7

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY
133gNhsqc
1413D HNCO, 3D HN(CA)CB, 3D HabCab(CO)NH, 3D HNCAHA, 3D HCCHCOSY (C13,1H,1H), 3D HCCHTOCSY (13C,13C,1H)
152CT gChsqc 2D spectra
NMR detailsText: Both aliphatic and aromatic 3D_13C-separated_NOESY were conducted

-
Sample preparation

Details
Solution-IDContentsSolvent system
11 mM TM1509 (100% 15N, 100% 13C), 450 mM NaCl, 25 mM NaHPO4, 10mM DTT, 0.01% NaN3, 1mM benzamidine, 1 x inhibitor cocktail pill, 95% H2O, 5% D2O95% H2O/5% D2O
21.2 mM TM1509 (100% 15N, 5% 13C), 450 mM NaCl, 25 mM NaHPO4, 10mM DTT, 0.01% NaN3, 1mM benzamidine, 1 x inhibitor cocktail pill, 95% H2O, 5% D2O95% H2O/5% D2O
31.2 mM TM1509 (100% 15N, 5% 13C), 450 mM NaCl, 25 mM NaHPO4, 10mM DTT, 0.01% NaN3, 1mM benzamidine, 1 x inhibitor cocktail pill, 95% H2O/5% D20 was titrated with D20 to reveal slowly exchanging amide protons95% H2O/5% D20 was titrated with D20 to reveal slowly exchanging amide protons
Sample conditionspH: 6.5 / Pressure: 1.0 atmosphere atm / Temperature: 298 K

-
NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA7501
Varian INOVAVarianINOVA6002

-
Processing

NMR software
NameVersionDeveloperClassification
DYANA1.5Guntert, Mumenthaler, Wuthrichstructure solution
CYANA1.05Hermann, Guntert, Wuthrichrefinement
MOLMOL1Koradi, R.; Billeter, M.; Wuthrich, K.data analysis
XEASY1.3.3Bartels, C.; Billeter, M.; Guntert, P.; Wuthrich, K.;data analysis
TALOS98.040.21.02Cornilescu, G.; Delaglio, F.; Bax, A.data analysis
RefinementMethod: DYANA 1.5 with 30,000 TAD steps, simulated annealing
Software ordinal: 1
NMR representativeSelection criteria: lowest target function
NMR ensembleConformer selection criteria: target function / 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://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