[English] 日本語
Yorodumi
- PDB-5xz0: Staphylococcal Enterotoxin B (SEB) mutant S19 - N23A, Y90A, R110A... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5xz0
TitleStaphylococcal Enterotoxin B (SEB) mutant S19 - N23A, Y90A, R110A and F177A
ComponentsStaphylococcal enterotoxin B
KeywordsTOXIN / Staphylococcal aureus / Enterotoxin / SEB
Function / homology
Function and homology information


: / toxin activity / extracellular region
Similarity search - Function
Staphylococcal enterotoxin/Streptococcal pyrogenic exotoxin signature 1. / Staphylococcal/streptococcal toxin, bacterial / Staphylococcal/Streptococcal toxin, OB-fold domain / Staphylococcal/Streptococcal toxin, beta-grasp domain / Staphylococcal/Streptococcal toxin, beta-grasp 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 ...Staphylococcal enterotoxin/Streptococcal pyrogenic exotoxin signature 1. / Staphylococcal/streptococcal toxin, bacterial / Staphylococcal/Streptococcal toxin, OB-fold domain / Staphylococcal/Streptococcal toxin, beta-grasp domain / Staphylococcal/Streptococcal toxin, beta-grasp 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
Staphylococcal enterotoxin B
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.002 Å
AuthorsJeong, W.H. / Song, D.H. / Hur, G.H. / Jeong, S.T.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
Agency for Defense Development07-203-603-005 Korea, Republic Of
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2017
Title: Structure of the staphylococcal enterotoxin B vaccine candidate S19 showing eliminated superantigen activity
Authors: Jeong, W.H. / Song, D.H. / Hur, G.H. / Jeong, S.T.
History
DepositionJul 11, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 1, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.page_first ..._citation.journal_abbrev / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Staphylococcal enterotoxin B
B: Staphylococcal enterotoxin B


Theoretical massNumber of molelcules
Total (without water)55,1942
Polymers55,1942
Non-polymers00
Water61334
1
A: Staphylococcal enterotoxin B


Theoretical massNumber of molelcules
Total (without water)27,5971
Polymers27,5971
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Staphylococcal enterotoxin B


Theoretical massNumber of molelcules
Total (without water)27,5971
Polymers27,5971
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)174.565, 174.630, 48.769
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222
Components on special symmetry positions
IDModelComponents
11B-93-

CYS

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111(chain A and (resid 9 through 53 or resid 55...
211(chain B and (resid 9 through 53 or resid 55...

-
Components

#1: Protein Staphylococcal enterotoxin B


Mass: 27597.080 Da / Num. of mol.: 2 / Fragment: UNP residues 29-263 / Mutation: N23A, Y90A, R110A, F177A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (strain COL) (bacteria)
Strain: COL / Gene: seb, SACOL0907 / Cell line (production host): BL21 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0H2WZB2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / 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: 3.37 Å3/Da / Density % sol: 63.47 % / Description: cubic, 0.05mm
Crystal growTemperature: 277 K / Method: evaporation / Details: 0.2M Potassium Fluoride 20% w/v PEG 3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97933 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 3.001→41.153 Å / Num. obs: 15421 / % possible obs: 99.8 % / Redundancy: 6.1 % / Net I/σ(I): 16.5
Reflection shellResolution: 3.0017→3.0534 Å / % possible all: 98

-
Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4C56, 4RGM

4c56

4rgm


Resolution: 3.002→41.153 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 22.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2429 1548 10.04 %
Rwork0.2037 --
obs0.2077 15415 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.002→41.153 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3668 0 0 34 3702
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033747
X-RAY DIFFRACTIONf_angle_d0.55045
X-RAY DIFFRACTIONf_dihedral_angle_d2.0422266
X-RAY DIFFRACTIONf_chiral_restr0.043528
X-RAY DIFFRACTIONf_plane_restr0.004646
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1692X-RAY DIFFRACTIONPOSITIONAL
12B1692X-RAY DIFFRACTIONPOSITIONAL0.015
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0017-3.09850.33231340.26761246X-RAY DIFFRACTION99
3.0985-3.20920.30841390.25011236X-RAY DIFFRACTION100
3.2092-3.33770.27181410.23761237X-RAY DIFFRACTION100
3.3377-3.48950.29451360.21971257X-RAY DIFFRACTION100
3.4895-3.67340.26441360.2021232X-RAY DIFFRACTION100
3.6734-3.90330.21481400.19611246X-RAY DIFFRACTION100
3.9033-4.20440.22341350.17351234X-RAY DIFFRACTION100
4.2044-4.6270.17921440.16441278X-RAY DIFFRACTION100
4.627-5.29540.20671420.16991276X-RAY DIFFRACTION100
5.2954-6.6670.22011450.20571281X-RAY DIFFRACTION100
6.667-41.15690.28671560.23431344X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.56210.9109-0.04571.56270.07941.8133-0.0544-0.42280.09290.0617-0.035-0.05050.48380.23780.03240.27120.0579-0.06240.15880.0190.274-41.3912-11.901916.0777
24.2321.7323-0.12132.8197-0.38732.162-0.0973-0.02030.457-0.00840.01420.31710.1361-0.06280.10380.25180.0003-0.02690.0725-0.04480.1942-50.4586-9.863811.76
34.21560.6833-0.41982.2903-0.42110.62380.0336-0.3534-0.625-0.0279-0.1534-0.16010.7371-0.1781-0.09130.3325-0.11660.0010.2507-0.03160.2675-51.4293-20.01814.6683
41.7181-1.0158-0.07444.17110.41072.6787-0.0789-0.101-0.09680.3455-0.00280.00970.1374-0.36210.05870.1784-0.0833-0.02070.22790.04130.2208-11.9133-45.889516.0578
54.21970.03570.25782.84491.43594.116-0.0702-0.2718-0.236-0.4823-0.0437-0.35110.3571-0.32440.14390.26590.01890.010.1448-0.02130.2318-6.8957-51.283712.8047
63.2452-1.1702-0.79044.17160.23871.930.0582-0.02720.30220.0341-0.0906-0.2738-0.288-0.02580.07410.16970.1154-0.03270.2360.07850.1975-13.9053-30.702511.1159
71.8597-0.87470.72513.54260.52091.0011-0.1625-0.1559-0.0930.4596-0.13820.6048-0.1938-0.72470.060.27640.01770.00360.2742-0.02580.2449-18.1445-37.265816.5044
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 77 )
2X-RAY DIFFRACTION2chain 'A' and (resid 78 through 183 )
3X-RAY DIFFRACTION3chain 'A' and (resid 184 through 236 )
4X-RAY DIFFRACTION4chain 'B' and (resid 2 through 77 )
5X-RAY DIFFRACTION5chain 'B' and (resid 78 through 120 )
6X-RAY DIFFRACTION6chain 'B' and (resid 121 through 199 )
7X-RAY DIFFRACTION7chain 'B' and (resid 200 through 236 )

+
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