[English] 日本語
Yorodumi
- PDB-8ykt: Fab and SEB complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8ykt
TitleFab and SEB complex
Components
  • Enterotoxin type B
  • Fab Heavy chain
  • Fab Light chain
KeywordsPROTEIN BINDING/IMMUNE SYSTEM / Fab / SEB / Complex / PROTEIN BINDING-IMMUNE SYSTEM complex
Function / homology
Function and homology information


toxin activity / extracellular region / metal ion binding
Similarity search - Function
Staphylococcal enterotoxin/Streptococcal pyrogenic exotoxin signature 1. / Staphylococcal/streptococcal toxin, bacterial / Staphylococcal/Streptococcal toxin, OB-fold / Staphylococcal/Streptococcal toxin, 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 / Superantigen toxin, C-terminal / Enterotoxin
Similarity search - Domain/homology
Biological speciesStaphylococcus aureus (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04 Å
AuthorsZeng, H. / Fan, H.Y.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32070941 China
National Natural Science Foundation of China (NSFC)32270989 China
CitationJournal: To Be Published
Title: Structure of Staphylococcal Enterotoxin B mutant in complex with a neutralization antibody Fab fragment
Authors: Fan, H.Y. / Zeng, H.
History
DepositionMar 5, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 12, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Enterotoxin type B
H: Fab Heavy chain
L: Fab Light chain


Theoretical massNumber of molelcules
Total (without water)76,0273
Polymers76,0273
Non-polymers00
Water7,548419
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)106.250, 73.320, 114.220
Angle α, β, γ (deg.)90.00, 91.66, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Enterotoxin type B / SEB


Mass: 28270.908 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: entB / Production host: Escherichia coli (E. coli) / References: UniProt: P01552
#2: Antibody Fab Heavy chain


Mass: 24824.789 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody Fab Light chain


Mass: 22931.410 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 419 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.92 Å3/Da / Density % sol: 57.94 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2M Lithum sulfate, 0.1M Sodium acetate pH5.5, 10%PEG1000, 10% PEG8000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Oct 26, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.04→38.33 Å / Num. obs: 55954 / % possible obs: 99.9 % / Redundancy: 6.8 % / CC1/2: 0.997 / Rmerge(I) obs: 0.155 / Rpim(I) all: 0.065 / Rrim(I) all: 0.168 / Χ2: 0.94 / Net I/σ(I): 10.4 / Num. measured all: 380788
Reflection shellResolution: 2.04→2.09 Å / % possible obs: 100 % / Redundancy: 7 % / Rmerge(I) obs: 1.405 / Num. measured all: 28725 / Num. unique obs: 4118 / CC1/2: 0.552 / Rpim(I) all: 0.573 / Rrim(I) all: 1.519 / Χ2: 0.99 / Net I/σ(I) obs: 1.7

-
Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.04→38.06 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2297 2878 5.14 %
Rwork0.1954 --
obs0.1972 55943 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.04→38.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5128 0 0 419 5547
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025287
X-RAY DIFFRACTIONf_angle_d0.5727185
X-RAY DIFFRACTIONf_dihedral_angle_d5.487720
X-RAY DIFFRACTIONf_chiral_restr0.045790
X-RAY DIFFRACTIONf_plane_restr0.004924
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.04-2.070.32971440.3092503X-RAY DIFFRACTION100
2.07-2.110.28681350.29152495X-RAY DIFFRACTION100
2.11-2.150.33241050.27462583X-RAY DIFFRACTION100
2.15-2.190.33351270.26332482X-RAY DIFFRACTION100
2.19-2.230.30171320.26142537X-RAY DIFFRACTION100
2.23-2.280.25621310.24942499X-RAY DIFFRACTION100
2.28-2.340.30721520.24922520X-RAY DIFFRACTION100
2.34-2.390.25541560.25332517X-RAY DIFFRACTION100
2.39-2.460.29351510.24332474X-RAY DIFFRACTION100
2.46-2.530.30981440.23222512X-RAY DIFFRACTION100
2.53-2.610.25451150.23642548X-RAY DIFFRACTION100
2.61-2.710.23981340.22392556X-RAY DIFFRACTION100
2.71-2.810.26511340.21662517X-RAY DIFFRACTION100
2.81-2.940.23441530.21292517X-RAY DIFFRACTION100
2.94-3.10.24711410.20782509X-RAY DIFFRACTION100
3.1-3.290.27331280.2022526X-RAY DIFFRACTION100
3.29-3.540.20651480.17672531X-RAY DIFFRACTION100
3.54-3.90.21211020.16812572X-RAY DIFFRACTION100
3.9-4.460.17571520.14092527X-RAY DIFFRACTION100
4.47-5.620.16221410.14792562X-RAY DIFFRACTION100
5.62-38.060.21711530.1822578X-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)
11.56730.58040.87772.81310.99611.7638-0.1659-0.05850.326-0.175-0.14350.6834-0.3285-0.40140.26830.4410.1046-0.10480.4378-0.04180.435521.98910.15859.2517
21.48470.63450.21452.19050.83470.62990.154-1.1744-0.21351.2452-0.52330.0923-0.4546-0.92080.32320.7842-0.0216-0.22310.9661-0.01161.0519.8634-12.98846.9822
34.20060.49971.3745.46980.02974.6083-0.0091-0.06810.3084-0.3818-0.18510.8614-0.5738-0.54730.21950.61260.0786-0.18290.4674-0.07970.505117.0176-8.3814-0.0985
43.30020.30721.59944.07330.62713.0133-0.05990.0480.1113-0.1845-0.08890.1257-0.2916-0.11960.09470.31790.017-0.02720.295-0.0070.204731.9936-3.227711.1794
52.6647-0.81561.24612.3983-0.39173.15460.10020.1195-0.2923-0.12020.04290.09360.27650.1218-0.10740.29490.0290.01810.2818-0.04290.272950.4809-26.877127.7163
63.1805-1.48422.54750.9798-1.4552.7159-0.15520.07210.1082-0.00970.0324-0.1308-0.13670.1423-0.03320.30660.00240.01950.2591-0.03680.247861.0867-21.33540.3963
71.8491-0.82850.22334.6142-0.32234.404-0.0307-0.0582-0.09130.1021-0.01670.1877-0.19440.08220.03430.190.01260.01680.22660.00130.30675.4468-26.874960.4817
81.5812-0.19650.17271.8321.65694.7867-0.06730.12920.0567-0.12530.0197-0.0099-0.23240.10760.05460.2263-0.0218-0.0010.230.02060.238651.5469-4.981835.1524
93.2558-1.7281-0.26763.68580.11521.55980.03230.181-0.0576-0.3256-0.1199-0.32910.10530.11670.08160.2527-0.01150.02610.24360.01190.285178.6373-13.966749.6283
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 48 )
2X-RAY DIFFRACTION2chain 'A' and (resid 49 through 63 )
3X-RAY DIFFRACTION3chain 'A' and (resid 64 through 130 )
4X-RAY DIFFRACTION4chain 'A' and (resid 131 through 238 )
5X-RAY DIFFRACTION5chain 'H' and (resid 2 through 99 )
6X-RAY DIFFRACTION6chain 'H' and (resid 100 through 146 )
7X-RAY DIFFRACTION7chain 'H' and (resid 147 through 227 )
8X-RAY DIFFRACTION8chain 'L' and (resid 2 through 111 )
9X-RAY DIFFRACTION9chain 'L' and (resid 112 through 214 )

+
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