[English] 日本語
Yorodumi
- PDB-1jor: Ensemble structures for unligated Staphylococcal nuclease-H124L -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1jor
TitleEnsemble structures for unligated Staphylococcal nuclease-H124L
Componentsstaphylococcal nuclease
KeywordsHYDROLASE / beta barrel / alpha helix
Function / homology
Function and homology information


3' overhang single-stranded DNA endodeoxyribonuclease activity / micrococcal nuclease / nucleic acid binding / extracellular region / metal ion binding / membrane
Similarity search - Function
OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #90 / Thermonuclease family signature 1. / Thermonuclease active site / Thermonuclease family signature 2. / Staphylococcal nuclease (SNase-like), OB-fold / Staphylococcal nuclease homologue / Thermonuclease domain profile. / Staphylococcal nuclease homologues / SNase-like, OB-fold superfamily / OB fold (Dihydrolipoamide Acetyltransferase, E2P) ...OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #90 / Thermonuclease family signature 1. / Thermonuclease active site / Thermonuclease family signature 2. / Staphylococcal nuclease (SNase-like), OB-fold / Staphylococcal nuclease homologue / Thermonuclease domain profile. / Staphylococcal nuclease homologues / SNase-like, OB-fold superfamily / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesStaphylococcus aureus (bacteria)
MethodSOLUTION NMR / Distance, hydrogen bond, torsion angle constraints
AuthorsWang, J. / Truckses, D.M. / Abildgaard, F. / Dzakula, Z. / Zolnai, Z. / Markley, J.L.
CitationJournal: J.Biomol.NMR / Year: 1997
Title: Solution structures of staphylococcal nuclease from multidimensional, multinuclear NMR: nuclease-H124L and its ternary complex with Ca2+ and thymidine-3',5'-bisphosphate.
Authors: Wang, J. / Truckses, D.M. / Abildgaard, F. / Dzakula, Z. / Zolnai, Z. / Markley, J.L.
History
DepositionJul 30, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 22, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 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
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: staphylococcal nuclease


Theoretical massNumber of molelcules
Total (without water)16,8181
Polymers16,8181
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)30 / 90structures with acceptable covalent geometry,structures with the least restraint violations
Representative

-
Components

#1: Protein staphylococcal nuclease / thermonuclease / tnase / micrococcal nuclease


Mass: 16818.340 Da / Num. of mol.: 1 / Fragment: nuclease A / Mutation: H124L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Plasmid: pTSN2cc / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL-21(DE3) / References: UniProt: P00644, micrococcal nuclease

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111E-COSY
222HMQC-J
133DQF-COSY
1412D NOESY
2542D NOESY
2623D 1H-15N NOESY-HMQC
2752D 1H-13C HMQC
286HNCO
2963D HNCA
1101and others

-
Sample preparation

Details
Solution-IDContentsSolvent system
13.5-5 mM Nuclease-H124L U-50% 2H; 300 mM KCl; D2OD2O
23.5-5 mM Nuclease-H124L U-95% 15N; 300 mM KCl; H2OH2O
33.5-5 mM Nuclease-H124L; 300 mM KCl; D2OD2O
43.5-5 mM Nuclease-H124L U-50% 2H; 300 mM KCl; H2OH2O
53.5-5 mM Nuclease-H124L U-98% 13C; 300 mM KCl; H2OH2O
63.5-5 mM Nuclease-H124L U-98% 13C U-99% 15N; 300 mM KCl; H2OH2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1300 nM KCl 5.5ambient 318 K
2300 nM KCl 5.1ambient 318 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AMBrukerAM5001
Bruker AMBrukerAM6002

-
Processing

NMR software
NameVersionDeveloperClassification
FelixBiosym Technologies Incprocessing
X-PLOR3.1Brungerstructure solution
Insight II2.3Biosym Technologies Incstructure solution
HBPLUSMcDonald and Thorntonstructure solution
X-PLOR3.1Brungerrefinement
RefinementMethod: Distance, hydrogen bond, torsion angle constraints / Software ordinal: 1
Details: 2176 constraints were used to calculate the structure
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry,structures with the least restraint violations
Conformers calculated total number: 90 / Conformers submitted total number: 30

+
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