[English] 日本語
Yorodumi
- PDB-1mpe: Ensemble of 20 structures of the tetrameric mutant of the B1 doma... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1mpe
TitleEnsemble of 20 structures of the tetrameric mutant of the B1 domain of streptococcal protein G
ComponentsImmunoglobulin G binding protein G
KeywordsPROTEIN BINDING / strand-exchanged tetramer / channel
Function / homology
Function and homology information


IgG binding / extracellular region
Similarity search - Function
IgG-binding B / B domain / Ubiquitin-like (UB roll) - #10 / 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. ...IgG-binding B / B domain / Ubiquitin-like (UB roll) - #10 / 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 / Ubiquitin-like (UB roll) / Roll / Alpha Beta
Similarity search - Domain/homology
Immunoglobulin G-binding protein G
Similarity search - Component
Biological speciesStreptococcus sp. 'group G' (bacteria)
MethodSOLUTION NMR / simulated annealing
Model type detailsminimized average
AuthorsFrank, M.K. / Dyda, F. / Dobrodumov, A. / Gronenborn, A.M.
Citation
Journal: Nat.Struct.Biol. / Year: 2002
Title: Core mutations switch monomeric protein GB1 into an intertwined tetramer.
Authors: Kirsten Frank, M. / Dyda, F. / Dobrodumov, A. / Gronenborn, A.M.
#1: Journal: Science / Year: 1991
Title: A Novel, Highly Stable Fold of the Immunoglobulin Binding Domain of Streptococcal Protein G.
Authors: Gronenborn, A.M. / Filpula, D.R. / Essig, N.Z. / Achari, A. / Whitlow, M. / Wingfield, P.T. / Clore, G.M.
#2: Journal: FEBS Lett. / Year: 1996
Title: Core Mutants of the Immunoglobulin Binding Domain of Streptococcal Protein G: Stability and Structural Integrity
Authors: Gronenborn, A.M. / Frank, M.K. / Clore, G.M.
History
DepositionSep 12, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 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: Immunoglobulin G binding protein G
B: Immunoglobulin G binding protein G
C: Immunoglobulin G binding protein G
D: Immunoglobulin G binding protein G


Theoretical massNumber of molelcules
Total (without water)25,2124
Polymers25,2124
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)21 / 100structures with least restraint violations and phi, psi angles of residue 46 in allowed region of Ramachrandran plot
RepresentativeModel #1minimized average structure

-
Components

#1: Antibody
Immunoglobulin G binding protein G / IgG binding protein G


Mass: 6302.931 Da / Num. of mol.: 4 / Fragment: B1 domain, sequence database residues 228-282 / Mutation: T2Q, L5V, A26F, F30V, Y33F, A34F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus sp. 'group G' (bacteria) / Gene: SPG / Plasmid: pet11a / Production host: Escherichia coli (E. coli) / Strain (production host): HMS174(DE3) / References: UniProt: P06654

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1123D 15N-separated NOESY
122HNHA
1313D 13C-separated NOESY
1434D 13C-separated NOESY
1514D 13C/15N-separated NOESY
1643D 12C-filtered 13C-separated NOESY
NMR detailsText: T1,T2, and heteronuclear NOEs collected. Dipolar couplings (N-H) were collected as well. Dipolar coupling and chemical shifts from residues with heteronuclear NOE below 0.6 were not used.

-
Sample preparation

Details
Solution-IDContentsSolvent system
13.5 mM (in monomer) U-15N,13C, 50 mM sodium phosphate buffer, 0.02% sodium azide90% H2O/10% D2O
22.89 mM (in monomer) U-15N, 50 mM sodium phosphate buffer, 0.02% sodium azide90% H2O/10% D2O
33.5 mM (in monomer) U-15N,13C, 50 mM sodium phosphate buffer, 0.02% sodium azide100% D2O
41.4 mM (in monomer) 1:1 mixture unlabelled:U-15N,13C, 50 mM sodium phosphate buffer, 0.02% sodium azide100% D2O
Sample conditionsIonic strength: 50 mM sodium phosphate, 0.02% sodium azide / pH: 5.45 / Pressure: 1 atm / Temperature: 313 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 DRXBrukerDRX8001
Bruker DMXBrukerDMX7502
Bruker DMXBrukerDMX6003
Bruker DMXBrukerDMX5004

-
Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2.2Frank Delaglioprocessing
PIPP4.3.2Dan Garrettdata analysis
XwinNMR2.6Bruker Corp.collection
X-PLOR4Brungerrefinement
CNS1Brungerstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
Details: NMR constraints (per monomer) 822 NOE-derived distance restraints (534 intramonomer, 288 intermonomer) 42 distance restraints from hydrogen bonds (20 intramonomer, 22 intermonomer) 30 J- ...Details: NMR constraints (per monomer) 822 NOE-derived distance restraints (534 intramonomer, 288 intermonomer) 42 distance restraints from hydrogen bonds (20 intramonomer, 22 intermonomer) 30 J-coupling restraints, 33 Residual dipolar couplings (HN) 66 backbone dihedral angle restraints 31 sidechain dihedral angle restraints
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with least restraint violations and phi, psi angles of residue 46 in allowed region of Ramachrandran plot
Conformers calculated total number: 100 / Conformers submitted total number: 21

+
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