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- PDB-4k09: Crystal structure of BbTX-II from Bothrops brazili venom -

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Basic information

Entry
Database: PDB / ID: 4k09
TitleCrystal structure of BbTX-II from Bothrops brazili venom
ComponentsBbTX-II
KeywordsTOXIN / Phospholipases A2
Function / homology
Function and homology information


calcium-dependent phospholipase A2 activity / arachidonic acid secretion / phospholipid metabolic process / lipid catabolic process / negative regulation of T cell proliferation / phospholipid binding / toxin activity / defense response to bacterium / calcium ion binding / extracellular region
Similarity search - Function
Phospholipase A2, aspartic acid active site / Phospholipase A2 aspartic acid active site. / Phospholipase A2 / Phospholipase A2, histidine active site / Phospholipase A2 histidine active site. / Phospholipase A2 / Phospholipase A2 domain / Phospholipase A2 / Phospholipase A2 / Phospholipase A2 domain ...Phospholipase A2, aspartic acid active site / Phospholipase A2 aspartic acid active site. / Phospholipase A2 / Phospholipase A2, histidine active site / Phospholipase A2 histidine active site. / Phospholipase A2 / Phospholipase A2 domain / Phospholipase A2 / Phospholipase A2 / Phospholipase A2 domain / Phospholipase A2 domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Basic phospholipase A2 homolog 2
Similarity search - Component
Biological speciesBothrops brazili (snake)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.107 Å
AuthorsFernandes, C.A.H. / Comparetti, E.J. / Borges, R.J. / Fontes, M.R.M.
CitationJournal: Biochim.Biophys.Acta / Year: 2013
Title: Structural bases for a complete myotoxic mechanism: Crystal structures of two non-catalytic phospholipases A2-like from Bothrops brazili venom.
Authors: Fernandes, C.A.H. / Comparetti, E.J. / Borges, R.J. / Huancahuire-Vega, S. / Ponce-Soto, L.A. / Marangoni, S. / Soares, A.M. / Fontes, M.R.M.
History
DepositionApr 3, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 20, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2013Group: Database references / Source and taxonomy / Structure summary

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BbTX-II
B: BbTX-II


Theoretical massNumber of molelcules
Total (without water)27,5622
Polymers27,5622
Non-polymers00
Water3,441191
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area960 Å2
ΔGint-11 kcal/mol
Surface area11740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.437, 56.437, 129.080
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein BbTX-II


Mass: 13781.146 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bothrops brazili (snake) / References: UniProt: I6L8L6*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 191 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsA SEQUENCE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST. NON-SEQUENTIAL RESIDUE NUMBERING IS ...A SEQUENCE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST. NON-SEQUENTIAL RESIDUE NUMBERING IS USED IN THIS ENTRY. MANY NUMBERS WERE SIMPLY SKIPPED IN THE NUMBERING AND HAVE NOTHING TO DO WITH LACK OF ELECTRON DENSITY.

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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: 2.15 Å3/Da / Density % sol: 42.87 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 30% (w/v) PEG 4000, 0.25M lithium sulfate, 0.1M Tris HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.435 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Apr 24, 2011
RadiationMonochromator: Single Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.435 Å / Relative weight: 1
ReflectionResolution: 2.107→32.3 Å / Num. obs: 13823 / % possible obs: 96 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.9 % / Biso Wilson estimate: 38.48 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 21.09

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Processing

Software
NameVersionClassificationNB
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
MAR345dtbdata collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.107→32.295 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.22 / σ(F): 1.34 / Phase error: 23.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2443 699 5.06 %
Rwork0.1936 --
obs0.196 13324 96.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.4949 Å2
Refinement stepCycle: LAST / Resolution: 2.107→32.295 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1788 0 0 191 1979
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041834
X-RAY DIFFRACTIONf_angle_d0.8352461
X-RAY DIFFRACTIONf_dihedral_angle_d11.521656
X-RAY DIFFRACTIONf_chiral_restr0.059265
X-RAY DIFFRACTIONf_plane_restr0.004322
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1068-2.26950.30151480.23342619X-RAY DIFFRACTION98
2.2695-2.49780.25891430.21162617X-RAY DIFFRACTION98
2.4978-2.8590.26631470.20962648X-RAY DIFFRACTION98
2.859-3.60130.23521300.18862636X-RAY DIFFRACTION96
3.6013-32.29930.22771310.1812604X-RAY DIFFRACTION90
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)
15.4889-0.33462.87442.3899-0.26975.09480.7914-0.13760.4852-0.353-0.48440.48120.939-1.0533-0.2090.34210.01310.01430.3380.03570.22223.4165-24.18-11.7293
23.23950.0655-1.16661.7983-0.7444.68250.4466-0.09191.13510.89740.0896-0.5673-0.4868-0.7916-0.26230.6134-0.03860.08370.20040.03590.405627.9771-18.3979-4.8324
31.4996-0.940.12651.4540.90112.31850.61250.74971.2976-0.72070.1281-0.7156-1.29710.27020.2960.7260.09270.33890.41870.26630.691932.5677-12.2961-16.5684
42.0201-0.3547-0.48541.2590.27952.63920.47650.69730.041-1.0082-0.16440.50290.5582-0.8818-0.20950.50360.0175-0.0420.57470.05840.338419.361-16.544-25.53
53.9008-2.4019-1.75493.4679-0.58583.03840.29910.93810.0988-0.3516-0.1347-0.04070.0774-0.0022-0.04230.38930.05240.05350.29740.1310.271924.359-27.887-19.519
60.025-0.06530.09840.15270.43271.0780.7530.60470.9154-0.73640.4705-0.44-1.85540.6918-0.10391.1164-0.10350.4230.2920.14920.963336.058-14.261-6.163
72.8633-1.1066-0.58234.9604-1.24452.1722-0.2345-0.0362-0.4637-0.31350.1003-0.51610.61770.01880.15170.39060.01630.06360.209-0.01660.334714.5764-5.8625-2.8476
82.7646-0.2898-0.01544.16831.43855.5531-0.1230.35070.0826-0.97580.1084-0.56310.16940.0584-0.02040.4249-0.00030.1140.25940.01680.29514.88298.4474-7.6532
92.19420.1929-0.45694.08651.36171.3928-0.3071-0.0163-0.1807-0.33680.1723-0.11650.5816-0.33010.08480.3139-0.00160.040.1697-0.02530.242510.8195.802-5.834
100.3430.5262-0.74980.6719-0.741.7203-0.9647-0.028-0.1238-0.4505-0.3014-0.76440.4640.27740.66180.8140.13450.23020.35150.01081.040914.765-12.595.244
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 1:13)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 15:21)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 22:52)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 53:71)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 72:107)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 108:121)
7X-RAY DIFFRACTION7(CHAIN B AND RESID 1:53)
8X-RAY DIFFRACTION8(CHAIN B AND RESID 57:79)
9X-RAY DIFFRACTION9(CHAIN B AND RESID 80:107)
10X-RAY DIFFRACTION10(CHAIN B AND RESID 108:121)

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