[English] 日本語
Yorodumi
- PDB-4owk: Crystal Structure of the Vibrio vulnificus Hemolysin/Cytolysin Be... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4owk
TitleCrystal Structure of the Vibrio vulnificus Hemolysin/Cytolysin Beta-Trefoil Lectin with N-Acetyl-D-Galactosamine Bound
ComponentsCytolysin
KeywordsTOXIN / lectin / pore-forming toxin / Beta-trefoil / R-type lectin
Function / homology
Function and homology information


cytolysis in another organism / toxin activity / carbohydrate binding / extracellular region
Similarity search - Function
Leukocidin/Hemolysin toxin / Leukocidin/Hemolysin toxin family / Leukocidin/porin MspA superfamily / Ricin-type beta-trefoil lectin domain / Ricin-type beta-trefoil / Lectin domain of ricin B chain profile. / Ricin B, lectin domain / Ricin B-like lectins / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) ...Leukocidin/Hemolysin toxin / Leukocidin/Hemolysin toxin family / Leukocidin/porin MspA superfamily / Ricin-type beta-trefoil lectin domain / Ricin-type beta-trefoil / Lectin domain of ricin B chain profile. / Ricin B, lectin domain / Ricin B-like lectins / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Mainly Beta
Similarity search - Domain/homology
2-acetamido-2-deoxy-beta-D-galactopyranose / Cytolysin
Similarity search - Component
Biological speciesVibrio vulnificus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsKaus, K. / Olson, R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1R15AI101977 United States
CitationJournal: J.Mol.Biol. / Year: 2014
Title: Glycan Specificity of the Vibrio vulnificus Hemolysin Lectin Outlines Evolutionary History of Membrane Targeting by a Toxin Family.
Authors: Kaus, K. / Lary, J.W. / Cole, J.L. / Olson, R.
History
DepositionFeb 2, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 28, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 30, 2014Group: Database references
Revision 1.2Feb 25, 2015Group: Derived calculations
Revision 1.3Oct 7, 2015Group: Other
Revision 1.4Sep 27, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.5Nov 1, 2017Group: Derived calculations / Category: pdbx_struct_assembly / Item: _pdbx_struct_assembly.method_details
Revision 1.6Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.7Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.8Dec 27, 2023Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cytolysin
B: Cytolysin
C: Cytolysin
D: Cytolysin
E: Cytolysin
F: Cytolysin
G: Cytolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,04220
Polymers107,9417
Non-polymers2,10113
Water15,223845
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Cytolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7333
Polymers15,4201
Non-polymers3132
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Cytolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6412
Polymers15,4201
Non-polymers2211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
C: Cytolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7333
Polymers15,4201
Non-polymers3132
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
D: Cytolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7333
Polymers15,4201
Non-polymers3132
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
E: Cytolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7333
Polymers15,4201
Non-polymers3132
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
F: Cytolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7333
Polymers15,4201
Non-polymers3132
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
G: Cytolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7333
Polymers15,4201
Non-polymers3132
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.389, 79.832, 148.694
Angle α, β, γ (deg.)90.000, 89.480, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Cytolysin


Mass: 15420.086 Da / Num. of mol.: 7 / Fragment: UNP residues 338-471
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio vulnificus (bacteria) / Strain: CMCP6 / Gene: VV2_0404,vvhA / Plasmid: pNGFP-BC / Production host: Escherichia coli (E. coli) / Strain (production host): NEB SHuffle T7 Express / References: UniProt: P19247
#2: Sugar
ChemComp-NGA / 2-acetamido-2-deoxy-beta-D-galactopyranose / N-acetyl-beta-D-galactosamine / 2-acetamido-2-deoxy-beta-D-galactose / 2-acetamido-2-deoxy-D-galactose / 2-acetamido-2-deoxy-galactose / N-ACETYL-D-GALACTOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGalpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-galactopyranosamineCOMMON NAMEGMML 1.0
b-D-GalpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 845 / 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: 3.08 Å3/Da / Density % sol: 60.06 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.25
Details: 100 mM TRIS, pH 8.25, 6% PEG 8000, 2 mM N-acetyl-D-galactosamine: Cryoprotected in 20% glycerol

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 16, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2→100 Å / Num. obs: 83325 / % possible obs: 95 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.161 / Χ2: 1.773 / Net I/av σ(I): 18.459 / Net I/σ(I): 6.2 / Num. measured all: 491799
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2-2.0740.86159600.60168.5
2.07-2.154.50.72375160.65286.1
2.15-2.255.30.58785890.6998.3
2.25-2.376.30.52686330.76799
2.37-2.526.30.37386940.92699.3
2.52-2.716.40.27586951.16699.7
2.71-2.996.40.20287211.66699.7
2.99-3.426.40.14487832.55399.8
3.42-4.316.30.10688023.49799.8
4.31-1006.30.09389323.72999.6

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO

-
Processing

Software
NameVersionClassification
HKL-2000704xdata reduction
PHASER2.5.5phasing
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.14data extraction
HKL-2000data scaling
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→37.172 Å / FOM work R set: 0.8912 / SU ML: 0.17 / σ(F): 1.35 / Phase error: 18.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1905 4166 5 %
Rwork0.1576 79132 -
obs0.1592 83298 95.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 171.9 Å2 / Biso mean: 36.18 Å2 / Biso min: 10.41 Å2
Refinement stepCycle: final / Resolution: 2→37.172 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7081 0 294 845 8220
Biso mean--59.67 42.93 -
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0117368
X-RAY DIFFRACTIONf_angle_d1.23310015
X-RAY DIFFRACTIONf_chiral_restr0.0561111
X-RAY DIFFRACTIONf_plane_restr0.0051295
X-RAY DIFFRACTIONf_dihedral_angle_d13.4292573
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.02280.2399820.22471787186965
2.0228-2.04660.25211060.21771837194366
2.0466-2.07150.24311210.19992026214774
2.0715-2.09770.24511260.20092146227278
2.0977-2.12530.21981210.18142356247786
2.1253-2.15450.23551310.18462633276495
2.1545-2.18520.19341420.17962686282899
2.1852-2.21780.19611510.16972736288797
2.2178-2.25250.2021530.167227232876100
2.2525-2.28940.22751540.16422683283799
2.2894-2.32890.2061410.156527722913100
2.3289-2.37120.1731310.15432749288099
2.3712-2.41680.19941610.15552752291399
2.4168-2.46620.17511450.157826842829100
2.4662-2.51980.21480.15932803295199
2.5198-2.57840.21841450.158727162861100
2.5784-2.64280.18911350.150228182953100
2.6428-2.71430.19621520.148727272879100
2.7143-2.79410.17181510.146827622913100
2.7941-2.88430.19451200.155928002920100
2.8843-2.98730.20541500.148227342884100
2.9873-3.10690.22241400.153128182958100
3.1069-3.24820.19531440.158627842928100
3.2482-3.41930.22941340.161927632897100
3.4193-3.63340.1881350.160228122947100
3.6334-3.91360.17811650.151227502915100
3.9136-4.30690.15711580.128327732931100
4.3069-4.92890.14041470.123327972944100
4.9289-6.20530.17031400.153828382978100
6.2053-37.17840.20481370.20152867300499
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)
12.4747-0.0091.21782.92930.64493.73470.033-0.1078-0.11250.05090.0478-0.04560.1473-0.2083-0.06910.3919-0.09830.03980.38890.01180.1643-43.2298-22.7514-20.116
24.8442.62971.16122.48080.5182.48730.1508-0.30590.35320.362-0.15630.27210.1076-0.16910.01140.343-0.02450.02630.2937-0.06120.2361-24.8023-3.6422-1.8084
33.16310.5987-1.09732.5399-1.38694.0652-0.02910.0681-0.03880.0429-0.0123-0.0231-0.3040.1170.04190.2927-0.0363-0.0290.2507-0.07660.1934-1.529117.0634-11.0388
41.92790.51690.8981.88040.69794.1966-0.2204-0.24520.18340.1123-0.0786-0.0942-0.74080.7480.21690.3686-0.0884-0.10260.38140.02410.24519.822122.9596-40.6174
52.37580.91190.50772.05660.46582.01370.03720.03-0.26290.0352-0.0413-0.25960.01630.05520.01740.1086-0.0186-0.00320.10640.0320.2562-0.00839.6277-68.6605
63.10231.0668-0.59933.2331-0.00421.49-0.06740.075-0.0159-0.07060.05210.03990.0636-0.0180.02160.08530.0070.00150.10180.02110.1484-24.2593-10.8327-73.6405
72.55840.46650.02072.144-0.14343.28790.1943-0.2654-0.09590.2879-0.20780.09560.2506-0.2828-0.00740.197-0.04970.02550.18160.00490.1512-43.6821-25.1268-52.3895
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA337 - 502
2X-RAY DIFFRACTION2chain BB337 - 501
3X-RAY DIFFRACTION3chain CC337 - 502
4X-RAY DIFFRACTION4chain DD337 - 502
5X-RAY DIFFRACTION5chain EE336 - 502
6X-RAY DIFFRACTION6chain FF336 - 502
7X-RAY DIFFRACTION7chain GG337 - 502

+
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