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- PDB-4wx5: pore-forming thermostable direct hemolysin from Grimontia hollisae -

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Basic information

Entry
Database: PDB / ID: 4wx5
Titlepore-forming thermostable direct hemolysin from Grimontia hollisae
ComponentsHemolysin, heat labile
KeywordsTOXIN / thermostable direct hemolysin / TDH / oligomerization
Function / homology
Function and homology information


hemolysis by symbiont of host erythrocytes / 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: 2.302 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
Water3,315184
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3000 Å2
ΔGint2 kcal/mol
Surface area28310 Å2
Unit cell
Length a, b, c (Å)105.343, 112.688, 60.902
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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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 / 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.: 184 / Source method: isolated from a natural source / Formula: H2O
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.

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.64 Å3/Da / Density % sol: 53.38 %
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

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 0.96379, 0.97904, 0.97920
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
10.963791
20.979041
30.97921
ReflectionResolution: 2.3→30 Å / Num. obs: 32500 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 8.1 % / Rmerge(I) obs: 0.083 / Rsym value: 0.083 / Net I/σ(I): 21.8
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.264 / Mean I/σ(I) obs: 6.7 / % possible all: 97.9

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassification
SCALEPACK2000data reduction
PHENIX1.9-1692phasing
PHENIX(phenix.refine: 1.8.3_1479)refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MAD / Resolution: 2.302→26.768 Å / FOM work R set: 0.7285 / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 31.48 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2407 1953 6.16 %Random selection
Rwork0.1934 29740 --
obs0.1964 31693 96.5 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 80.31 Å2 / Biso mean: 31.36 Å2 / Biso min: 10.95 Å2
Refinement stepCycle: final / Resolution: 2.302→26.768 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4803 0 0 184 4987
Biso mean---32.13 -
Num. residues----616
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074976
X-RAY DIFFRACTIONf_angle_d1.0086781
X-RAY DIFFRACTIONf_chiral_restr0.04743
X-RAY DIFFRACTIONf_plane_restr0.004888
X-RAY DIFFRACTIONf_dihedral_angle_d13.6411758
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3018-2.35930.32691110.25221886199787
2.3593-2.42310.3121460.23811996214293
2.4231-2.49430.30621340.22442040217494
2.4943-2.57480.23771320.22162068220095
2.5748-2.66670.30251430.2142086222996
2.6667-2.77340.28961420.20872122226497
2.7734-2.89950.2631370.20862123226097
2.8995-3.05210.28631380.21142139227798
3.0521-3.24310.28361410.1992145228698
3.2431-3.4930.26041410.22184232599
3.493-3.84360.23261470.18982195234299
3.8436-4.39760.20121410.15822214235599
4.3976-5.53250.1581460.1542226237298
5.5325-26.76980.20321540.19022316247099

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