[English] 日本語
Yorodumi
- PDB-1gb4: HYPERTHERMOPHILIC VARIANT OF THE B1 DOMAIN FROM STREPTOCOCCAL PRO... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1gb4
TitleHYPERTHERMOPHILIC VARIANT OF THE B1 DOMAIN FROM STREPTOCOCCAL PROTEIN G, NMR, 47 STRUCTURES
ComponentsGB1-C3B4
KeywordsHYPERTHERMOPHILE / STREPTOCOCCAL PROTEIN G
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 / Ubiquitin-like (UB roll) - #10 / Immunoglobulin/albumin-binding domain superfamily / YSIRK Gram-positive signal peptide / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. ...IgG-binding B / B domain / M protein-type anchor domain / GA-like domain / GA-like domain / Ubiquitin-like (UB roll) - #10 / 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 / Ubiquitin-like (UB roll) / Roll / Alpha Beta
Similarity search - Domain/homology
Immunoglobulin G-binding protein G
Similarity search - Component
Biological speciesStreptococcus sp. (bacteria)
MethodSOLUTION NMR / distance geometry
AuthorsMalakauskas, S.M. / Mayo, S.L.
CitationJournal: Nat.Struct.Biol. / Year: 1998
Title: Design, structure and stability of a hyperthermophilic protein variant.
Authors: Malakauskas, S.M. / Mayo, S.L.
History
DepositionJan 19, 1998Processing site: BNL
Revision 1.0Jul 22, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Other
Category: database_2 / pdbx_database_status / 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.process_site / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: GB1-C3B4


Theoretical massNumber of molelcules
Total (without water)6,3671
Polymers6,3671
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)47 / 75NO RESTRAINT VIOLATIONS GREATER THAN 0.3 ANGSTROMS
Representative

-
Components

#1: Protein GB1-C3B4


Mass: 6367.060 Da / Num. of mol.: 1 / Fragment: B1 DOMAIN / Mutation: V1M, Y4F, V7I, T17I, T19I, T26E, V30I, V40I
Source method: isolated from a genetically manipulated source
Details: HYPERTHERMOPHILIC VARIANT OF THE B1 DOMAIN FROM STREPTOCOCCAL PROTEIN G
Source: (gene. exp.) Streptococcus sp. (bacteria) / Strain: G148 / Cell line: BL21 / Gene: GB1C3B4 / Plasmid: PET-GB1C3B4 / Species (production host): Escherichia coli / Gene (production host): GB1C3B4 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P19909

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: DQF-COSY NOESY TOCSY

-
Sample preparation

DetailsContents: H2O/D2O
Sample conditionsIonic strength: 50mM / pH: 5.0 / Pressure: ATMOSPHERIC atm / Temperature: 308 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

NMR spectrometerType: Varian UNITYPLUS / Manufacturer: Varian / Model: UNITYPLUS / Field strength: 600 MHz

-
Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
NMR software
NameVersionDeveloperClassification
X-PLOR3.1BRUNGERrefinement
ANSIGstructure solution
VARIAN VNMRVNMRstructure solution
RefinementMethod: distance geometry / Software ordinal: 1
NMR ensembleConformer selection criteria: NO RESTRAINT VIOLATIONS GREATER THAN 0.3 ANGSTROMS
Conformers calculated total number: 75 / Conformers submitted total number: 47

+
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