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- PDB-4k06: Crystal structure of MTX-II from Bothrops brazili venom complexed... -

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Basic information

Entry
Database: PDB / ID: 4k06
TitleCrystal structure of MTX-II from Bothrops brazili venom complexed with polyethylene glycol
ComponentsMTX-II
KeywordsTOXIN / Phospholipase 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
Chem-7PE / TRIETHYLENE GLYCOL / Basic phospholipase A2 homolog 2
Similarity search - Component
Biological speciesBothrops brazili (snake)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.08 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 13, 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

Downloads & links

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Assembly

Deposited unit
A: MTX-II
B: MTX-II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,80210
Polymers27,5062
Non-polymers1,2958
Water4,522251
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3820 Å2
ΔGint-66 kcal/mol
Surface area12090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.010, 71.414, 44.420
Angle α, β, γ (deg.)90.000, 102.500, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein MTX-II


Mass: 13753.136 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bothrops brazili (snake) / References: UniProt: I6L8L6*PLUS

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Non-polymers , 5 types, 259 molecules

#2: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-PE4 / 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL / POLYETHYLENE GLYCOL PEG4000


Mass: 354.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H34O8 / Comment: precipitant*YM
#5: Chemical ChemComp-7PE / 2-(2-(2-(2-(2-(2-ETHOXYETHOXY)ETHOXY)ETHOXY)ETHOXY)ETHOXY)ETHANOL / POLYETHYLENE GLYCOL FRAGMENT


Mass: 310.384 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H30O7
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 251 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.2 Å3/Da / Density % sol: 43.99 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 30% (w/v) PEG 8000, 0.25M Ammonium sulfate, 0.1M sodium cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING 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: 2.08→20 Å / Num. all: 13821 / Num. obs: 13752 / % possible obs: 96.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.8 % / Biso Wilson estimate: 20.8 Å2 / Rmerge(I) obs: 0.129 / Net I/σ(I): 5.29

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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: 2.08→19.017 Å / Occupancy max: 1 / Occupancy min: 0.78 / SU ML: 0.16 / σ(F): 0.07 / Phase error: 23.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2362 693 5.04 %
Rwork0.1927 --
obs0.195 13751 95.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.2752 Å2
Refinement stepCycle: LAST / Resolution: 2.08→19.017 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1837 0 76 251 2164
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041959
X-RAY DIFFRACTIONf_angle_d0.8612607
X-RAY DIFFRACTIONf_dihedral_angle_d12.944734
X-RAY DIFFRACTIONf_chiral_restr0.059265
X-RAY DIFFRACTIONf_plane_restr0.004328
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0801-2.24040.26421410.21672599X-RAY DIFFRACTION96
2.2404-2.46550.24621420.20052669X-RAY DIFFRACTION98
2.4655-2.82120.25331440.20292628X-RAY DIFFRACTION97
2.8212-3.55070.22391370.19172643X-RAY DIFFRACTION96
3.5507-19.01750.22231290.17712519X-RAY DIFFRACTION91
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)
10.5656-0.0718-0.85030.0978-0.03681.1167-0.02320.1503-0.1679-0.3329-0.0002-0.04250.154-0.1818-0.00170.18690.019-0.01620.16510.00720.14955.668-3.8462-14.1441
20.38430.00140.37130.75290.26190.2169-0.2616-0.2586-0.01730.00730.2407-0.1261-0.4460.0474-0.00070.20520.00780.01220.19330.00680.158510.01446.7924-7.6769
30.202-0.1013-0.0920.3428-0.24850.3497-0.0644-0.0007-0.2539-0.5462-0.2095-0.870.2070.4157-0.03270.25610.05570.06250.32830.06170.343722.7491.298-4.657
40.10860.0504-0.09080.11490.14010.4090.1263-0.0918-0.70480.1208-0.1958-0.13770.22270.0321-0.01270.22460.0012-0.04230.22160.02810.259316.235-10.305-10.851
50.4097-0.0852-0.52790.5175-0.02630.85830.0645-0.05350.058-0.0819-0.0359-0.106-0.0735-0.06360.01410.13680.024-0.00480.1389-0.00630.161813.057-8.695-4.155
61.16290.5333-0.36412.4725-0.55840.2052-0.8636-0.32960.0407-1.1860.56370.0487-0.29440.587-0.04270.3675-0.0862-0.04550.42290.01350.1859-2.7960.086-6.467
70.0795-0.08710.02780.04850.00940.00630.09590.18680.0270.18430.1477-0.2393-0.11810.49220.00040.39440.0365-0.01880.2106-0.05350.316-1.6448.586-16.738
80.4484-0.26960.79980.3002-0.15232.8012-0.1023-0.08360.14010.1487-0.02920.2038-0.0236-0.05420.02270.145-0.04210.04080.1538-0.01110.211713.404114.4997-27.6276
90.33780.4180.2040.95210.26930.1636-0.0288-0.1659-0.09550.66890.04230.72620.28730.0052-0.00650.2289-0.0360.03120.22540.02450.15716.72135.0039-28.9111
100.01690.00420.02990.00350.00710.0332-0.1079-0.4044-0.09430.6836-0.151-0.18440.04640.05670.00040.3057-0.02580.05340.25430.01650.429113.9652-1.6225-26.8034
110.24130.2201-0.66670.2506-0.68932.09570.0901-0.102-0.00790.36410.1213-0.0630.2238-0.27340.04610.24890.0075-0.00090.1995-0.03480.271915.507-6.069-31.738
120.2569-0.16940.00140.13640.09330.119-0.12480.4656-0.1641-0.16930.0806-0.2394-0.06750.1189-0.00040.18280.0192-0.01010.17850.01240.194119.26021.8732-33.2393
130.4209-0.2505-0.21230.2995-0.0590.24710.0542-0.25380.55150.788-0.1173-0.4935-0.10820.01340.00720.3695-0.0015-0.09390.28360.04180.216230.7756.678-27.058
140.08530.02370.17930.01080.02020.32180.13940.55120.4404-0.0836-0.2286-0.16680.25590.2136-0.0290.1477-0.0199-0.04030.18770.05760.30620.65117.611-26.737
150.29510.34270.35480.4136-0.24620.9045-0.14320.2984-0.07160.00560.0931-0.0511-0.09390.0412-0.02780.1374-0.01240.00750.1132-0.00130.154421.91214.657-32.606
160.27530.11480.28960.77130.23250.2684-0.0419-0.6505-0.17810.4240.12690.46160.0856-0.1485-0.0390.391-0.09280.08320.2863-0.02340.25885.8384.726-38.973
170.1852-0.36050.10521.4334-0.47741.5275-0.5649-0.0375-1.05440.3921-0.0419-0.39920.29570.3919-0.72720.28820.00280.08870.2583-0.02510.48293.124-3.45-30.104
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 1:26)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 27:53)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 57:61)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 67:79)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 80:107)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 108:114)
7X-RAY DIFFRACTION7(CHAIN A AND RESID 115:121)
8X-RAY DIFFRACTION8(CHAIN B AND RESID 1:13)
9X-RAY DIFFRACTION9(CHAIN B AND RESID 15:26)
10X-RAY DIFFRACTION10(CHAIN B AND RESID 27:31)
11X-RAY DIFFRACTION11(CHAIN B AND RESID 32:38)
12X-RAY DIFFRACTION12(CHAIN B AND RESID 39:53)
13X-RAY DIFFRACTION13(CHAIN B AND RESID 57:61)
14X-RAY DIFFRACTION14(CHAIN B AND RESID 67:79)
15X-RAY DIFFRACTION15(CHAIN B AND RESID 80:107)
16X-RAY DIFFRACTION16(CHAIN B AND RESID 108:114)
17X-RAY DIFFRACTION17(CHAIN B AND RESID 115:121)

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