[English] 日本語
Yorodumi
- PDB-2klk: Solution structure of GB1 A34F mutant with RDC and SAXS -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2klk
TitleSolution structure of GB1 A34F mutant with RDC and SAXS
ComponentsIMMUNOGLOBULIN G-BINDING PROTEIN G
KeywordsIMMUNE SYSTEM / GB1 A34F Variant / RDC / SAXS / PROTEIN BINDING
Function / homology
Function and homology information


IgG binding / extracellular region
Similarity search - Function
IgG-binding B / B domain / M protein-type anchor domain / GA-like domain / GA-like domain / Immunoglobulin/albumin-binding domain superfamily / YSIRK Gram-positive signal peptide / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain
Similarity search - Domain/homology
Immunoglobulin G-binding protein G
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodSOLUTION SCATTERING / SOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsWang, J. / Zuo, X. / Yu, P. / Byeon, I.L. / Jung, J. / Schwieters, C.D. / Gronenborn, A.M. / Wang, Y.
CitationJournal: J.Am.Chem.Soc. / Year: 2009
Title: Determination of multicomponent protein structures in solution using global orientation and shape restraints.
Authors: Wang, J. / Zuo, X. / Yu, P. / Byeon, I.J. / Jung, J. / Wang, X. / Dyba, M. / Seifert, S. / Schwieters, C.D. / Qin, J. / Gronenborn, A.M. / Wang, Y.X.
History
DepositionJul 6, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 6, 2009Provider: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: IMMUNOGLOBULIN G-BINDING PROTEIN G
B: IMMUNOGLOBULIN G-BINDING PROTEIN G


Theoretical massNumber of molelcules
Total (without water)12,6102
Polymers12,6102
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)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Antibody IMMUNOGLOBULIN G-BINDING PROTEIN G


Mass: 6304.905 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P06654*PLUS

-
Experimental details

-
Experiment

Experiment
Method
SOLUTION SCATTERING
SOLUTION NMR
NMR experimentType: 2D 1H-15N HSQC

-
Sample preparation

Details
Solution-IDContentsSolvent system
12.2 mM [U-100% 15N] entity_1-1, 95% H2O/5% D2O95% H2O/5% D2O
20.3 mM entity_1-2, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
2.2 mMentity_1-1[U-100% 15N]1
0.3 mMentity_1-22
Sample conditionsIonic strength: 0.10 / pH: 5.5 / Pressure: ambient / Temperature: 298 K

-
Data collection

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 800 MHz
Soln scatterType: x-ray / Buffer name: 20 MM NACL 20 MM MES / Conc. range: 1.0-3.6 / Data analysis software list: GNOM
Data reduction software list: MARDETECTOR,HOME-WRITTEN PROGRAM
Detector specific: HOME-MADE / Detector type: CCD CAMERA / Mean guiner radius: 1.46 nm / Mean guiner radius esd: 0.03 nm / Num. of time frames: 20 / Protein length: 0.5 / Sample pH: 5.5 / Source beamline: 12-ID / Source class: Y / Source type: APS ARGONNE / Temperature: 298 K

-
Processing

NMR softwareName: X-PLOR NIH / Version: 2.22 / Developer: Schwieters, Kuszewski, Tjandra and Clore / Classification: refinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10
Soln scatter modelConformer selection criteria: STRUCTURES WITH THE LOWEST ENERGY
Num. of conformers calculated: 100 / Num. of conformers submitted: 10 / Representative conformer: 1 / Software list: GNOM

+
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