[English] 日本語
Yorodumi
- PDB-1m4v: Crystal structure of SET3, a superantigen-like protein from Staph... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1m4v
TitleCrystal structure of SET3, a superantigen-like protein from Staphylococcus aureus
ComponentsSET3, superantigen-like protein
KeywordsIMMUNE SYSTEM / OB-fold / Beta-grasp / superantigen fold
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 / Ubiquitin-like (UB roll) - #120 / Superantigen toxin, C-terminal / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #110 / Enterotoxin ...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 / 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 / MIR / Resolution: 1.9 Å
AuthorsArcus, V.L. / Langley, R. / Proft, T. / Fraser, J.D. / Baker, E.N.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: The three-dimensional structure of a superantigen-like protein, SET3, from a pathogenicity island of the Staphylococcus aureus genome
Authors: Arcus, V.L. / Langley, R. / Proft, T. / Fraser, J.D. / Baker, E.N.
History
DepositionJul 5, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site
Remark 999SEQUENCE The conflicts between the sequence for this structure and the database sequence arise from ...SEQUENCE The conflicts between the sequence for this structure and the database sequence arise from the allelic variation between Staphylococcus aureus strains seen for some of these superantigen-like proteins.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: SET3, superantigen-like protein
B: SET3, superantigen-like protein


Theoretical massNumber of molelcules
Total (without water)48,4302
Polymers48,4302
Non-polymers00
Water6,792377
1
A: SET3, superantigen-like protein


Theoretical massNumber of molelcules
Total (without water)24,2151
Polymers24,2151
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: SET3, superantigen-like protein


Theoretical massNumber of molelcules
Total (without water)24,2151
Polymers24,2151
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.123, 65.123, 196.731
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

-
Components

#1: Protein SET3, superantigen-like protein / exotoxin-like protein


Mass: 24214.842 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: SET3 / Plasmid: pET32a_3C / Production host: Escherichia coli (E. coli) / Strain (production host): AD494 / References: UniProt: Q9ZFS6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 377 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 4

-
Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50.3 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: HEPES, ammonium sulphate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120 mMsodium phosphate1droppH6.0
212 mg/mlSET31drop
350 mMHEPES1reservoirpH7.0
41.5 Mammonium sulfate1reservoiror 50mM HEPES, pH7.0
50.9 Msodium potassium tartrate1reservoir

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11101
21101
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
SYNCHROTRONEMBL/DESY, HAMBURG BW7A10.8452
ROTATING ANODERIGAKU RUH3R21.5418
Detector
TypeIDDetectorDateDetails
MARRESEARCH1AREA DETECTORJan 1, 2001
MARRESEARCH2AREA DETECTORFeb 10, 2001mirrors
RadiationMonochromator: Ni filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.84521
21.54181
ReflectionResolution: 1.9→30 Å / Num. all: 37131 / Num. obs: 35700 / % possible obs: 96.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.3 % / Biso Wilson estimate: 7.2 Å2 / Rmerge(I) obs: 0.108 / Net I/σ(I): 12.1
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.458 / Mean I/σ(I) obs: 2.75 / Num. unique all: 3548 / % possible all: 95.6
Reflection
*PLUS
Lowest resolution: 30 Å

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNS1refinement
RefinementMethod to determine structure: MIR / Resolution: 1.9→29.17 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2261080.28 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.24 1792 5 %RANDOM
Rwork0.205 ---
obs0.205 35694 96.2 %-
all-35700 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 52.8386 Å2 / ksol: 0.414541 e/Å3
Displacement parametersBiso mean: 16.5 Å2
Baniso -1Baniso -2Baniso -3
1-1.18 Å21.9 Å20 Å2
2--1.18 Å20 Å2
3----2.36 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 1.9→29.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3300 0 0 377 3677
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d25.1
X-RAY DIFFRACTIONc_improper_angle_d0.66
X-RAY DIFFRACTIONc_mcbond_it1.081.5
X-RAY DIFFRACTIONc_mcangle_it1.592
X-RAY DIFFRACTIONc_scbond_it1.792
X-RAY DIFFRACTIONc_scangle_it2.682.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.282 290 4.9 %
Rwork0.226 5593 -
obs-5593 95.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
Refinement
*PLUS
Lowest resolution: 30 Å / Rfactor Rfree: 0.24
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.66
LS refinement shell
*PLUS
Lowest resolution: 1.97 Å

+
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://pdbjlvh1.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