[English] 日本語
Yorodumi
- PDB-2jv2: Solution Structure of the N-terminal Domain of PH1500 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2jv2
TitleSolution Structure of the N-terminal Domain of PH1500
ComponentsPutative uncharacterized protein PH1500
KeywordsUNKNOWN FUNCTION / AAA ATPASE NC-DOMAIN-LIKE
Function / homology
Function and homology information


: / Domain of unknown function (DUF6849) / Vcp-like ATPase; Chain A, domain 2 - #10 / Vcp-like ATPase; Chain A, domain 2 / CDC48, domain 2 / Cell division protein 48 (CDC48), domain 2 / Cell division protein 48 (CDC48) domain 2 / CDC48 domain 2-like superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
CDC48 domain-containing protein
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodSOLUTION NMR / simulated annealing
Model type detailsminimized average
AuthorsVarnay, I. / Truffault, V. / Coles, M.
CitationJournal: To be Published
Title: The Solution Structure of Ph1500-N
Authors: Varnay, I. / Djuranovic, S. / Truffault, V. / Lupas, A. / Kessler, H. / Coles, M.
History
DepositionSep 11, 2007Deposition site: BMRB / Processing site: RCSB
SupersessionSep 25, 2007ID: 2I7M
Revision 1.0Sep 25, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: 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
Revision 1.3May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative uncharacterized protein PH1500


Theoretical massNumber of molelcules
Total (without water)9,4491
Polymers9,4491
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)22 / 50target function
RepresentativeModel #1minimized average structure

-
Components

#1: Protein Putative uncharacterized protein PH1500


Mass: 9449.224 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: cis-P66, cis-P68 / Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Gene: PH1500 / Production host: Escherichia coli (E. coli) / References: UniProt: O59169

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1223D 15N-SEPARATED NOESY
132HNHA
142HNHB
153CNH-NOESY
1633D 13C-SEPARATED NOESY
1733D CBCA(CO)NH
1833D HN(CA)CB
1933D HNCO
11033D (H)CCH-TOCSY

-
Sample preparation

Details
Solution-IDContentsSolvent system
11 mM HYPOTHETICAL PROTEIN PH1500, 50 mM PHOSPHATE BUFFER, 50 mM sodium chloride, 90 % H2O, 10 % D2O, 90% H2O/10% D2O90% H2O/10% D2O
21 mM [U-100% 15N] HYPOTHETICAL PROTEIN PH1500, 50 mM PHOSPHATE BUFFER, 50 mM sodium chloride, 90 % H2O, 10 % D2O, 90% H2O/10% D2O90% H2O/10% D2O
31 mM [U-100% 13C; U-100% 15N] HYPOTHETICAL PROTEIN PH1500, 50 mM PHOSPHATE BUFFER, 50 mM sodium chloride, 90 % H2O, 10 % D2O, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMHYPOTHETICAL PROTEIN PH15001
50 mMPHOSPHATE BUFFER1
50 mMsodium chloride1
90 %H2O1
10 %D2O1
1 mMHYPOTHETICAL PROTEIN PH1500[U-100% 15N]2
50 mMPHOSPHATE BUFFER2
50 mMsodium chloride2
90 %H2O2
10 %D2O2
1 mMHYPOTHETICAL PROTEIN PH1500[U-100% 13C; U-100% 15N]3
50 mMPHOSPHATE BUFFER3
50 mMsodium chloride3
90 %H2O3
10 %D2O3
Sample conditionsIonic strength: 50 / pH: 7 / Pressure: AMBIENT / Temperature: 300 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
BRUKER DMXBrukerDMX6001
BRUKER DMXBrukerDMX9002

-
Processing

NMR software
NameVersionDeveloperClassification
X-PLOR NIH2.9.4ABRUNGER, A.T. et al.structure solution
X-PLOR NIH2.9.4ABRUNGER, A.T. et al.refinement
XwinNMR3.6Brukercollection
XwinNMR3.6Brukerprocessing
Sparky3.11Goddard, T.D. et al.data analysis
RefinementMethod: simulated annealing / Software ordinal: 1
Details: Protocol including conformational database potential, BASED ON 748 DISTANCE RESTRAINTS, TALOS RESTRAINTS FOR 55 RESIDUES, 47 SIDECHAIN CHI1 AND 11 SIDECHAIN CHI2 DIHEDRAL RESTRAINTS, 34 ...Details: Protocol including conformational database potential, BASED ON 748 DISTANCE RESTRAINTS, TALOS RESTRAINTS FOR 55 RESIDUES, 47 SIDECHAIN CHI1 AND 11 SIDECHAIN CHI2 DIHEDRAL RESTRAINTS, 34 HBOND RESTRAINTS AND 51 PHI AND 16 PSI J-COUPLING RESTRAINTS.
NMR constraintsNOE constraints total: 786 / NOE intraresidue total count: 194 / NOE long range total count: 193 / NOE medium range total count: 96 / NOE sequential total count: 269 / Protein chi angle constraints total count: 51 / Protein other angle constraints total count: 19 / Protein phi angle constraints total count: 58 / Protein psi angle constraints total count: 58
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 50 / Conformers submitted total number: 22

+
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