[English] 日本語
Yorodumi
- PDB-1v1o: staphylococcal superantigen-like protein 7 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1v1o
Titlestaphylococcal superantigen-like protein 7
ComponentsEXOTOXIN 1
KeywordsVIRULENCE FACTOR / ANTIGEN PRESENTING CELL / SECRETED PROTEIN / STAPHYLOCOCCAL EXOTOXIN 1 / SET1
Function / homology
Function and homology information


extracellular region
Similarity search - Function
Staphylococcus aureus exotoxin / Staphylococcal superantigen-like OB-fold domain / Staphylococcal superantigen-like OB-fold domain / Staphylococcal enterotoxin/Streptococcal pyrogenic exotoxin, conserved site / Staphyloccocal enterotoxin/Streptococcal pyrogenic exotoxin signature 2. / Superantigen, staphylococcal/streptococcal toxin, bacterial / Staphylococcal/Streptococcal toxin, beta-grasp domain / Staphylococcal/Streptococcal toxin, beta-grasp domain / Ubiquitin-like (UB roll) - #120 / Superantigen toxin, C-terminal ...Staphylococcus aureus exotoxin / Staphylococcal superantigen-like OB-fold domain / Staphylococcal superantigen-like OB-fold domain / Staphylococcal enterotoxin/Streptococcal pyrogenic exotoxin, conserved site / Staphyloccocal enterotoxin/Streptococcal pyrogenic exotoxin signature 2. / Superantigen, staphylococcal/streptococcal toxin, bacterial / Staphylococcal/Streptococcal toxin, beta-grasp domain / Staphylococcal/Streptococcal toxin, beta-grasp domain / Ubiquitin-like (UB roll) - #120 / Superantigen toxin, C-terminal / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #110 / Enterotoxin / Ubiquitin-like (UB roll) / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Roll / Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesSTAPHYLOCOCCUS AUREUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.75 Å
AuthorsNaylor, C.E. / Briggs, D.C. / Nair, S.P. / Al-Shangiti, A.M.
CitationJournal: Infect.Immun. / Year: 2004
Title: Structural Relationships and Cellular Tropism of Staphylococcal Superantigen-Like Proteins
Authors: Al-Shangiti, A.M. / Naylor, C.E. / Nair, S.P. / Briggs, D.C. / Henderson, B. / Chain, B.
History
DepositionApr 21, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 1, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: EXOTOXIN 1
B: EXOTOXIN 1


Theoretical massNumber of molelcules
Total (without water)48,9572
Polymers48,9572
Non-polymers00
Water64936
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)81.660, 81.660, 148.040
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.99854, -0.01102, 0.05297), (0.00398, -0.99134, -0.13124), (0.05396, -0.13084, 0.98993)
Vector: -2.73221, 37.48265, 2.51646)
DetailsTHE ABOVE OLIGOMERIC STATE WAS DETERMINED FROM THEDEPOSITED COORDINATES USING THE PROTEIN QUATERNARYSTRUCTURE (PQS) ALGORITHM. HOWEVER, THE AUTHORS OF THISPDB ENTRY STRESS THAT THE BIOLOGICALLY SIGNIFICANT STATEFOR THIS ENTRY IS UNKNOWN AT THE TIME OF DEPOSITION.

-
Components

#1: Protein EXOTOXIN 1 / STAPHYLOCOCCAL SUPERANTIGEN LIKE PROTEIN 7


Mass: 24478.357 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STAPHYLOCOCCUS AUREUS (bacteria) / Strain: NCTC6571 / Plasmid: PQE30 / Production host: ESCHERICHIA COLI K-12 (bacteria) / Variant (production host): JM109(PREP4) / References: UniProt: Q9ZFS5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSIGNAL SEQUENCE REMOVED, HIS-TAG ADDED

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 56 %
Crystal growpH: 6.5
Details: 28% PEG-MME 2K, 0.2 M AMMONIUM SULPHATE, 0.1 M MES, PH 6.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9788
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 15, 1999 / Details: 2 MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9788 Å / Relative weight: 1
ReflectionResolution: 2.75→45.5 Å / Num. obs: 59998 / % possible obs: 98.7 % / Redundancy: 4.5 % / Biso Wilson estimate: 73.7 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 14.5
Reflection shellResolution: 2.75→2.9 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 3.1 / % possible all: 99.2

-
Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MAD
Starting model: PDB ENTRY 1M4V

1m4v


Resolution: 2.75→39.36 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 1375631.4 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MLF
Details: NCS GROUP 1 IS N-TERMINAL DOMAIN (18-105), GROUP 2 IS C-TERMINAL DOMAIN (115-211)
RfactorNum. reflection% reflectionSelection details
Rfree0.259 663 5 %RANDOM
Rwork0.213 ---
obs0.213 13374 97.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 30.2925 Å2 / ksol: 0.357508 e/Å3
Displacement parametersBiso mean: 45.5 Å2
Baniso -1Baniso -2Baniso -3
1--5.64 Å20 Å20 Å2
2---5.64 Å20 Å2
3---11.27 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.42 Å0.43 Å
Refinement stepCycle: LAST / Resolution: 2.75→39.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3142 0 0 36 3178
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.67
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it3.053.5
X-RAY DIFFRACTIONc_mcangle_it4.434.5
X-RAY DIFFRACTIONc_scbond_it4.784.5
X-RAY DIFFRACTIONc_scangle_it6.446
Refine LS restraints NCSRms dev Biso : 2.02 Å2 / Rms dev position: 0.29 Å / Weight Biso : 2 / Weight position: 20
LS refinement shellResolution: 2.75→2.92 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.322 124 5.7 %
Rwork0.301 2053 -
obs--98.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAMWATER.TOP

+
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