[English] 日本語
Yorodumi
- PDB-2m6q: Refined Solution NMR Structure of Staphylococcus aureus protein S... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2m6q
TitleRefined Solution NMR Structure of Staphylococcus aureus protein SAV1430. Northeast Strucutral Genomics Consortium Target ZR18
ComponentsSAV1430
KeywordsUNKNOWN FUNCTION / Structural Genomics / NORTHEAST STRUCTURAL GENOMICS CONSORTIUM / NESG / PSI-Biology / Protein Structure Initiative
Function / homology
Function and homology information


Scaffold protein Nfu/NifU, N-terminal domain / Scaffold protein Nfu/NifU, N-terminal / Scaffold protein Nfu/NifU, N-terminal domain superfamily / Scaffold protein Nfu/NifU N terminal / Scaffold protein Nfu/NifU N terminal / Ribosomal Protein S8; Chain: A, domain 1 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Scaffold protein Nfu/NifU N-terminal domain-containing protein / Nfu_N domain-containing protein
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsBaran, M.C. / Aramini, J.M. / Huang, Y.J. / Xiao, R. / Acton, T.B. / Shih, L. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG)
Citation
Journal: J.Biomol.Nmr / Year: 2013
Title: PDBStat: a universal restraint converter and restraint analysis software package for protein NMR.
Authors: Tejero, R. / Snyder, D. / Mao, B. / Aramini, J.M. / Montelione, G.T.
#1: Journal: J.Am.Chem.Soc. / Year: 2006
Title: FAST-NMR: functional annotation screening technology using NMR spectroscopy.
Authors: Mercier, K.A. / Baran, M. / Ramanathan, V. / Revesz, P. / Xiao, R. / Montelione, G.T. / Powers, R.
History
DepositionApr 8, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 1, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 21, 2013Group: Database references
Revision 1.2Feb 5, 2014Group: Database references
Revision 1.3Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / 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_status.status_code_nmr_data / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.4May 15, 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: SAV1430


Theoretical massNumber of molelcules
Total (without water)10,4881
Polymers10,4881
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)10 / 56structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein SAV1430


Mass: 10487.755 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria)
Strain: Mu50 / Gene: SAV1430 / Plasmid: ZR18-21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21MGK / References: UniProt: Q99U58, UniProt: A0A0H3JRL4*PLUS

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR / Details: Refinement of PDB 1PQX
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
112NH HSQC
122HNCO
132HN(CA)CB
142HN(CO)CACB
152HNCA
162HN(CO)CA
172HCC(CO)NH-TOCSY
182H(CCCO)NH-TOCSY
192(HA)CA(CO)NH
1102HACANH
1112CH HSQC
1122(H)CCH-COSY
113213C EDITED NOESY
1142(HB)CB(CGCD)HD RD
1152AROMATICTOCSY RD
1161hetNOE
1171HNHA
118215N EDITED NOESY
1191CH HSQC high res.

-
Sample preparation

Details
Solution-IDContentsSolvent system
11.3 mM [U-100% 15N; U-5% 13C] ZR18, 20 mM MES, 100 mM NaCl, 5 mM CaCl2, 10 mM DTT, 0.02 % NaN3, 95% H2O/5% D2O95% H2O/5% D2O
21.15 mM [U-100% 15N; U-100% 13C] ZR18, 20 mM MES, 100 mM NaCl, 5 mM CaCl2, 10 mM DTT, 0.02 % NaN3, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.3 mMZR18-1[U-100% 15N; U-5% 13C]1
20 mMMES-21
100 mMNaCl-31
5 mMCaCl2-41
10 mMDTT-51
0.02 %NaN3-61
1.15 mMZR18-7[U-100% 15N; U-100% 13C]2
20 mMMES-82
100 mMNaCl-92
5 mMCaCl2-102
10 mMDTT-112
0.02 %NaN3-122
Sample conditionsIonic strength: 0.1 / pH: 6.5 / Temperature: 298 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian UNITY InovaVarianUNITY Inova5001
Varian UNITY InovaVarianUNITY Inova6002

-
Processing

NMR software
NameVersionDeveloperClassification
HYPER3.2Tejero, Monleon, Celda, Powers and Montelionedata analysis
TALOS2.1Cornilescu, Delaglio and Baxdata analysis
VNMR6.1CVariandata collection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxraw spectral data processing
SparkyGoddardspectral visualization
AutoAssignZimmerman, Moseley, Kulikowski and Montelioneautomated backbone assignments
AutoStructure1.1.2Huang, Tejero, Powers and Montelioneautomated structural determination
SPINSBaran, Montelioneintegrated spectral analysus software
SPINSBaran, Montelioneintegrated spectral analysus software
CNSrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: Refinement of PDB 1PQX coordinates (10 models) using CNS in explicit water. The original 1PQX models were generated by AutoStructure.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 56 / Conformers submitted total number: 10

+
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