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- PDB-3u3u: Crystal structure of the tablysin-15-leukotriene E4 complex -

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Basic information

Entry
Database: PDB / ID: 3u3u
TitleCrystal structure of the tablysin-15-leukotriene E4 complex
ComponentsTablysin 15
KeywordsPROTEIN BINDING / CAP domain / binding protein / integrin alphaVbeta3 and leukotriene E4
Function / homology
Function and homology information


toxin activity / extracellular region
Similarity search - Function
Venom allergen 3, insect / Pathogenesis-related Protein p14a / CAP / SCP / Tpx-1 / Ag5 / PR-1 / Sc7 family of extracellular domains. / CAP domain / Cysteine-rich secretory protein family / CAP superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CITRIC ACID / Chem-EAH / PRASEODYMIUM ION / Tablysin 15
Similarity search - Component
Biological speciesTabanus yao (insect)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.5 Å
AuthorsAndersen, J.F.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Structure of protein having inhibitory disintegrin and leukotriene scavenging functions contained in single domain.
Authors: Xu, X. / Francischetti, I.M. / Lai, R. / Ribeiro, J.M. / Andersen, J.F.
History
DepositionOct 6, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2012Provider: repository / Type: Initial release
Revision 1.1May 23, 2012Group: Database references
Revision 1.2Oct 17, 2012Group: Database references
Revision 1.3Jan 28, 2015Group: Other

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: Tablysin 15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,9225
Polymers26,0771
Non-polymers8464
Water1,69394
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.774, 69.774, 85.473
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11C-322-

HOH

21C-324-

HOH

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Components

#1: Protein Tablysin 15


Mass: 26076.619 Da / Num. of mol.: 1 / Fragment: unp residues 24-255
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tabanus yao (insect) / Plasmid: pET17b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysE / References: UniProt: F8QQG5
#2: Chemical ChemComp-PR / PRASEODYMIUM ION


Mass: 140.908 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Pr
#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#4: Chemical ChemComp-EAH / (5S,7E,9E,11Z,14Z)-5-hydroxyicosa-7,9,11,14-tetraenoic acid


Mass: 320.466 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H32O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / Source method: isolated from a natural source / Formula: H2O

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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: 2.3 Å3/Da / Density % sol: 46.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 10 % PEG 6000, 100 mM citrate, 13 mM praseodymium (III) acetate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-002+ / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jul 7, 2011
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→18.22 Å / Num. all: 8629 / Num. obs: 8629 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.054 / Χ2: 0.96 / Net I/σ(I): 14.5 / Scaling rejects: 242
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
2.5-2.593.670.1438.131388451.2499.8
2.59-2.693.680.1179.231978591.299.8
2.69-2.813.720.110.731288291.2599.9
2.81-2.963.740.08811.332638661.0899.9
2.96-3.153.750.0661432408590.89100
3.15-3.393.740.05615.731578410.8199.8
3.39-3.733.750.06114.932648690.86100
3.73-4.263.770.04420.832848680.73100
4.26-5.343.680.04519.732888900.6999.6
5.34-18.223.550.04820.132439030.8796.9

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Processing

Software
NameVersionClassificationNB
d*TREK9.7 W8RSSIdata scaling
d*TREK9.7 W8RSSIdata reduction
PHENIX1.7.1_743refinement
PDB_EXTRACT3.1data extraction
CrystalCleardata collection
PHASERphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.5→17.446 Å / Occupancy max: 1 / Occupancy min: 0.42 / SU ML: 0.78 / σ(F): 1.35 / Phase error: 23.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2528 410 4.76 %
Rwork0.2021 --
obs0.2044 8622 99.49 %
all-8622 -
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 35.494 Å2 / ksol: 0.328 e/Å3
Displacement parametersBiso max: 109.77 Å2 / Biso mean: 44.4724 Å2 / Biso min: 18.23 Å2
Baniso -1Baniso -2Baniso -3
1--0.5793 Å2-0 Å20 Å2
2---0.5793 Å20 Å2
3---1.1586 Å2
Refinement stepCycle: LAST / Resolution: 2.5→17.446 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1816 0 50 94 1960
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0131911
X-RAY DIFFRACTIONf_angle_d1.2522569
X-RAY DIFFRACTIONf_chiral_restr0.074269
X-RAY DIFFRACTIONf_plane_restr0.006344
X-RAY DIFFRACTIONf_dihedral_angle_d16.349732
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)
12.5101-1.234-0.16852.15040.36021.9015-0.1029-0.3930.05180.25190.1684-0.15910.0060.0003-0.05930.1797-0.0038-0.03990.2474-0.03420.214321.74723.0463.4161
21.1649-0.673-0.23392.50110.72351.6024-0.2409-1.16-0.64210.7124-0.09131.03370.547-0.9802-0.03540.5-0.0783-0.02980.55420.15490.637715.2457-11.40298.6427
31.9264-1.04930.12161.9846-0.16052.19970.0101-0.1248-0.17890.0757-0.0064-0.17310.27360.1674-0.05590.1967-0.0123-0.0560.24810.04620.210725.4163-7.74812.8641
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'C' and (resseq 3:119)C3 - 119
2X-RAY DIFFRACTION2chain 'C' and (resseq 120:155)C120 - 155
3X-RAY DIFFRACTION3chain 'C' and (resseq 156:234)C156 - 234

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