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- PDB-3u3n: Crystal structure of tablysin-15 -

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Basic information

Entry
Database: PDB / ID: 3u3n
TitleCrystal structure of tablysin-15
ComponentsTablysin 15
KeywordsPROTEIN BINDING / CAP domain / Binding protein / alphaVbeta3 integrin / salivary gland
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 / PALMITIC ACID / PRASEODYMIUM ION / Tablysin 15
Similarity search - Component
Biological speciesTabanus yao (insect)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.651 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
Revision 1.4Nov 8, 2017Group: Refinement description / Category: software

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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)26,8585
Polymers26,0771
Non-polymers7824
Water3,873215
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Tablysin 15
hetero molecules

C: Tablysin 15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,71610
Polymers52,1532
Non-polymers1,5638
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-1/31
Buried area5250 Å2
ΔGint-17 kcal/mol
Surface area21160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.598, 69.598, 86.132
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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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-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H32O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 215 / 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: 2.31 Å3/Da / Density % sol: 46.74 %
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: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 0.99999 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 14, 2010
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99999 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. all: 29066 / Num. obs: 29066 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.9 % / Biso Wilson estimate: 19.1 Å2 / Rmerge(I) obs: 0.062 / Χ2: 1.31 / Net I/σ(I): 11.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.65-1.68100.51714210.858199.9
1.68-1.7112.50.46914490.9221100
1.71-1.7414.10.41114560.9051100
1.74-1.7814.50.3314590.9031100
1.78-1.8214.60.27314510.8871100
1.82-1.8614.80.23514480.9641100
1.86-1.913.40.22714641.0631100
1.9-1.9614.70.16614721.21100
1.96-2.0114.80.13814601.0261100
2.01-2.0814.80.10714551.0171100
2.08-2.1514.80.09514831.1071100
2.15-2.2414.20.09414611.231100
2.24-2.3412.40.08214261.566197.1
2.34-2.4614.80.06314751.2671100
2.46-2.6214.80.05714761.3641100
2.62-2.8214.80.05414841.5041100
2.82-3.1114.60.05314772.0261100
3.11-3.5513.80.05114892.542197.9
3.55-4.4811.10.03711522.15175.9
4.48-5013.50.0316081.863199.6

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.7.1_743refinement
PDB_EXTRACT3.1data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.651→32.265 Å / Occupancy max: 1 / Occupancy min: 0.32 / FOM work R set: 0.8624 / SU ML: 0.44 / σ(F): 1.34 / Phase error: 20.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2245 1472 5.08 %
Rwork0.1903 --
obs0.192 28988 98.32 %
all-28988 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 32.671 Å2 / ksol: 0.334 e/Å3
Displacement parametersBiso max: 71.79 Å2 / Biso mean: 26.2175 Å2 / Biso min: 7.46 Å2
Baniso -1Baniso -2Baniso -3
1--0.0548 Å20 Å20 Å2
2---0.0548 Å20 Å2
3---0.1097 Å2
Refinement stepCycle: LAST / Resolution: 1.651→32.265 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1789 0 45 215 2049
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121897
X-RAY DIFFRACTIONf_angle_d0.9642577
X-RAY DIFFRACTIONf_chiral_restr0.066268
X-RAY DIFFRACTIONf_plane_restr0.004335
X-RAY DIFFRACTIONf_dihedral_angle_d15.196733
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6512-1.70450.29531320.257825072639100
1.7045-1.76540.23991210.223824852606100
1.7654-1.8360.23961430.196225112654100
1.836-1.91960.23551260.203725042630100
1.9196-2.02080.22041470.190424972644100
2.0208-2.14740.20211260.183825392665100
2.1474-2.31310.21251500.19272472262298
2.3131-2.54580.19711280.187225292657100
2.5458-2.9140.27191580.201325542712100
2.914-3.67050.22071230.18182411253493
3.6705-32.27130.20981180.17812507262592
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)
12.3011-1.0051-0.11642.8867-1.18743.56890.08850.1399-0.234-0.2174-0.07780.17430.3896-0.1934-0.08690.1387-0.0078-0.01490.12940.00240.1189-20.0827-11.0093-10.6046
22.2494-1.2538-0.63021.75470.92082.3529-0.142-0.3787-0.2110.20270.39950.16860.22620.25620.06770.13750.05720.01360.21630.07890.197-18.193-13.81711.153
32.0054-0.59230.12952.4647-0.22382.0188-0.0541-0.36340.21660.26230.13320.1144-0.6415-0.0401-0.1710.22790.05480.07940.173-0.01070.1359-28.89549.56238.9255
42.0772-1.31910.32481.1844-0.84032.0665-0.00810.04140.004-0.0286-0.0355-0.04740.11670.0731-0.06780.1023-0.0036-0.00620.09980.0010.102-20.8779-5.8112-2.6485
51.5248-0.59480.68261.2786-0.47332.1831-0.1455-0.4924-0.03820.38010.2248-0.09010.07470.41220.05480.17320.0768-0.02160.29050.00320.0791-14.486-4.97916.488
62.21560.412-0.60924.6896-1.54232.8671-0.1415-0.61080.41080.62290.1567-0.2067-0.58140.4512-0.04030.30220.0344-0.0640.4195-0.11420.1828-16.5467.86414.664
70.95160.01550.17921.6715-0.03230.75180.0799-0.0110.43010.065-0.0181-0.2617-0.35140.14480.07550.4231-0.25350.19150.1654-0.08310.5551-14.395517.64651.7344
81.533-0.88820.09751.5401-0.4271.5565-0.0774-0.28920.10630.17710.1915-0.0667-0.11020.24570.03460.06330.0293-0.010.14-0.00920.0316-17.9854-1.16227.1454
90.81410.0211-0.13961.1152-0.34351.34340.32410.07860.56590.0183-0.0824-0.1002-0.8076-0.1753-0.1730.47510.05160.18270.090.07430.2857-25.129317.1044-2.4135
100.8734-0.7746-0.82480.76971.05852.14560.16690.16640.1297-0.0095-0.1620.3182-0.6097-0.5874-0.07520.24140.08980.0820.2254-0.01170.2039-35.2019.1122.501
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'C' and (resseq 3:22)C3 - 22
2X-RAY DIFFRACTION2chain 'C' and (resseq 23:38)C23 - 38
3X-RAY DIFFRACTION3chain 'C' and (resseq 39:75)C39 - 75
4X-RAY DIFFRACTION4chain 'C' and (resseq 76:105)C76 - 105
5X-RAY DIFFRACTION5chain 'C' and (resseq 106:119)C106 - 119
6X-RAY DIFFRACTION6chain 'C' and (resseq 120:136)C120 - 136
7X-RAY DIFFRACTION7chain 'C' and (resseq 137:155)C137 - 155
8X-RAY DIFFRACTION8chain 'C' and (resseq 156:190)C156 - 190
9X-RAY DIFFRACTION9chain 'C' and (resseq 191:210)C191 - 210
10X-RAY DIFFRACTION10chain 'C' and (resseq 211:234)C211 - 234

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