[English] 日本語
Yorodumi
- PDB-4wx3: pore-forming thermostable direct hemolysin from Grimontia hollisae -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4wx3
Titlepore-forming thermostable direct hemolysin from Grimontia hollisae
ComponentsHemolysin, heat labile
KeywordsTOXIN / thermostable direct hemolysin / TDH / tetramer / oligomeriation
Function / homology
Function and homology information


symbiont-mediated hemolysis of host erythrocyte / toxin activity / extracellular region
Similarity search - Function
Vibrio parahaemolyticus thermostable direct hemolysin / Thermostable direct haemolysin, vibrio / Thermostable direct haemolysin superfamily / Vibrio thermostable direct hemolysin / Mutm (Fpg) Protein; Chain: A, domain 2 / Sandwich / Mainly Beta
Similarity search - Domain/homology
Hemolysin, heat labile
Similarity search - Component
Biological speciesGrimontia hollisae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.701 Å
AuthorsWang, Y.-K. / Wu, T.-K. / Li, T.-H.T.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
National Science CouncilNSC101-2113-M-005-017-MY2 Taiwan
CitationJournal: To be published
Title: Multiple pleomorphic tetramers of pore-forming thermostable direct hemolysin from Grimontia hollisae in exerting membrane binding and hemolytic activity
Authors: Wang, Y.-K. / Huang, S.-C. / Huang, W.-T. / Chang, C.-Y. / Kuo, T.-M. / Yip, B.-S. / Wu, T.-K. / Li, T.-H.T.
History
DepositionNov 13, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 18, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_prerelease_seq / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _pdbx_struct_oper_list.symmetry_operation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Hemolysin, heat labile
B: Hemolysin, heat labile
C: Hemolysin, heat labile
D: Hemolysin, heat labile


Theoretical massNumber of molelcules
Total (without water)74,5744
Polymers74,5744
Non-polymers00
Water4,324240
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5200 Å2
ΔGint-10 kcal/mol
Surface area26030 Å2
Unit cell
Length a, b, c (Å)105.297, 112.588, 60.803
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein
Hemolysin, heat labile


Mass: 18643.596 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Grimontia hollisae (bacteria) / Plasmid: pCR2.1-TOPO / Details (production host): pCR2.1-TOPO / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)(pLysS) / References: UniProt: P14711
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 240 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE AUTHORS USED GRIMONTIA HOLLISAE STRAIN ATCC33564. THE AUTHORS ARE CONVINCED OF THIS SEQUENCE BY ...THE AUTHORS USED GRIMONTIA HOLLISAE STRAIN ATCC33564. THE AUTHORS ARE CONVINCED OF THIS SEQUENCE BY THE ELECTRON DENSITY MAP.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density % sol: 53.73 % / Description: thin flat plate
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 28%(v/v) PEG 400, 0.2 M CaCl2, 0.1 M Na-HEPES buffer

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 0.9789, 0.9790, 0.9639
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 15, 2010
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97891
20.9791
30.96391
ReflectionResolution: 1.7→30 Å / Num. obs: 73925 / % possible obs: 92.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.9 % / Rmerge(I) obs: 0.064 / Rsym value: 0.064 / Net I/σ(I): 4.3
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 4.3 / % possible all: 79.3

-
Phasing

PhasingMethod: MAD
Phasing MADD res high: -0 Å / D res low: 0 Å / FOM : 0 / Reflection: 0

-
Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.4_1496)refinement
SCALEPACK2000data reduction
PHENIX1.9-1692phasing
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MAD / Resolution: 1.701→23.848 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 31.5 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2336 1877 2.72 %Random selection
Rwork0.2011 ---
obs0.202 69101 86.27 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.701→23.848 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4759 0 0 240 4999
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054939
X-RAY DIFFRACTIONf_angle_d0.8476736
X-RAY DIFFRACTIONf_dihedral_angle_d12.591725
X-RAY DIFFRACTIONf_chiral_restr0.033743
X-RAY DIFFRACTIONf_plane_restr0.003880
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7006-1.74660.4024850.3133877X-RAY DIFFRACTION65
1.7466-1.7980.33131470.30844515X-RAY DIFFRACTION76
1.798-1.8560.34011390.27314844X-RAY DIFFRACTION82
1.856-1.92230.32381350.24725004X-RAY DIFFRACTION85
1.9223-1.99920.26161410.23285242X-RAY DIFFRACTION88
1.9992-2.09020.31671660.21785370X-RAY DIFFRACTION91
2.0902-2.20030.24411430.19935378X-RAY DIFFRACTION90
2.2003-2.3380.2271600.19735398X-RAY DIFFRACTION90
2.338-2.51840.2781400.19935439X-RAY DIFFRACTION91
2.5184-2.77150.2551600.20415509X-RAY DIFFRACTION92
2.7715-3.17170.22181510.19825521X-RAY DIFFRACTION92
3.1717-3.9930.20191570.17645563X-RAY DIFFRACTION91
3.993-23.85060.16071530.16785564X-RAY DIFFRACTION88

+
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