[English] 日本語
Yorodumi
- PDB-5bmi: Nitroxide Spin Labels in Protein GB1: T44 Mutant, Crystal Form A -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5bmi
TitleNitroxide Spin Labels in Protein GB1: T44 Mutant, Crystal Form A
ComponentsImmunoglobulin G-binding protein G
KeywordsIMMUNE SYSTEM / Bacterial Proteins / Electron Spin Resonance Spectroscopy
Function / homology
Function and homology information


IgG binding / cell wall / 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
Chem-MTN / Immunoglobulin G-binding protein G
Similarity search - Component
Biological speciesStreptococcus sp. group G (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsCunningham, T.C. / Horne, W.S. / Saxena, S.
CitationJournal: Protein Sci. / Year: 2016
Title: Rotameric preferences of a protein spin label at edge-strand beta-sheet sites.
Authors: Cunningham, T.F. / Pornsuwan, S. / Horne, W.S. / Saxena, S.
History
DepositionMay 22, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 6, 2016Provider: repository / Type: Initial release
Revision 1.1May 4, 2016Group: Database references

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Immunoglobulin G-binding protein G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,4952
Polymers6,2311
Non-polymers2641
Water27015
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area110 Å2
ΔGint-3 kcal/mol
Surface area3970 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)24.979, 37.507, 26.350
Angle α, β, γ (deg.)90.00, 108.24, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

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


Mass: 6230.848 Da / Num. of mol.: 1 / Fragment: UNP residues 304-357 / Mutation: T44C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus sp. group G (bacteria) / Gene: spg / Production host: Escherichia coli (E. coli) / References: UniProt: P19909
#2: Chemical ChemComp-MTN / S-[(1-oxyl-2,2,5,5-tetramethyl-2,5-dihydro-1H-pyrrol-3-yl)methyl] methanesulfonothioate / MTSL / MTSL


Mass: 264.385 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C10H18NO3S2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 1.81 Å3/Da / Density % sol: 32.04 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1 M HEPES pH 7.5, 1.2 M sodium citrate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Mar 12, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→25.03 Å / Num. obs: 1575 / % possible obs: 96.1 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 13.6
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.228 / Mean I/σ(I) obs: 2.3 / % possible all: 95.9

-
Processing

Software
NameVersionClassification
CrystalCleardata reduction
CrystalCleardata scaling
PHENIX1.8.1_1168refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB 2QMT
Resolution: 2.5→25.025 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.48 / Phase error: 34.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2507 72 4.59 %
Rwork0.235 --
obs0.2358 1568 95.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→25.025 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms449 0 0 15 464
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003456
X-RAY DIFFRACTIONf_angle_d1.026622
X-RAY DIFFRACTIONf_dihedral_angle_d15.816164
X-RAY DIFFRACTIONf_chiral_restr0.05471
X-RAY DIFFRACTIONf_plane_restr0.00178
LS refinement shellHighest resolution: 2.5001 Å
RfactorNum. reflection% reflection
Rfree0.2507 72 -
Rwork0.235 1496 -
obs--96 %

+
About Yorodumi

-
News

-
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

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

Result of Omokage search can be filtered by keywords and the database types

Related info.:Omokage search

-
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