- PDB-3ux7: Crystal structure of a dimeric myotoxic component of the Vipera a... -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 3ux7
Title
Crystal structure of a dimeric myotoxic component of the Vipera ammodytes meridionalis venom reveals determinants of myotoxicity and membrane damaging activity
Components
Ammodytin L(1) isoform
Keywords
TOXIN / Snake venom / Ser49 myotoxin
Function / homology
Function and homology information
phospholipase A2 activity / arachidonate secretion / phospholipid metabolic process / lipid catabolic process / 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
Mass: 18.015 Da / Num. of mol.: 90 / Source method: isolated from a natural source / Formula: H2O
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Experimental details
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Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
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Sample preparation
Crystal
Density Matthews: 2.16 Å3/Da / Density % sol: 42.93 %
Crystal grow
Method: vapor diffusion, hanging drop Details: Single crystals suitable for X-ray analysis were obtained after 5 days by the hanging-drop vapour-diffusion technique, using a protein solution with concentration of 10mg/ml in water. The ...Details: Single crystals suitable for X-ray analysis were obtained after 5 days by the hanging-drop vapour-diffusion technique, using a protein solution with concentration of 10mg/ml in water. The reservoir solution contained 25.5% PEG-4000, 0.17 M ammonium sulphate and 15% glycerol., VAPOR DIFFUSION, HANGING DROP
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.8123 Å / Relative weight: 1
Reflection
Resolution: 2.95→40 Å / Num. obs: 21213
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Processing
Software
Name
Version
Classification
DNA
datacollection
PHASER
phasing
REFMAC
5.6.0117
refinement
DENZO
datareduction
SCALEPACK
datascaling
Refinement
Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.97→40 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.914 / SU B: 15.611 / SU ML: 0.301 / Cross valid method: THROUGHOUT / ESU R Free: 0.52 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.26079
972
5.1 %
RANDOM
Rwork
0.22439
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-
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obs
0.22626
17915
97.05 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parameters
Biso mean: 27.764 Å2
Baniso -1
Baniso -2
Baniso -3
1-
3.77 Å2
-0 Å2
-0.61 Å2
2-
-
-1.71 Å2
0 Å2
3-
-
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-2.07 Å2
Refinement step
Cycle: LAST / Resolution: 2.97→40 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
7463
0
95
90
7648
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.008
0.02
7728
X-RAY DIFFRACTION
r_bond_other_d
X-RAY DIFFRACTION
r_angle_refined_deg
1.279
1.973
10398
X-RAY DIFFRACTION
r_angle_other_deg
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.876
5
968
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
37.622
24.153
301
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
18.532
15
1360
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
20.067
15
24
X-RAY DIFFRACTION
r_chiral_restr
0.085
0.2
1071
X-RAY DIFFRACTION
r_gen_planes_refined
0.004
0.021
5684
X-RAY DIFFRACTION
r_gen_planes_other
X-RAY DIFFRACTION
r_nbd_refined
X-RAY DIFFRACTION
r_nbd_other
X-RAY DIFFRACTION
r_nbtor_refined
X-RAY DIFFRACTION
r_nbtor_other
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
X-RAY DIFFRACTION
r_xyhbond_nbd_other
X-RAY DIFFRACTION
r_metal_ion_refined
X-RAY DIFFRACTION
r_metal_ion_other
X-RAY DIFFRACTION
r_symmetry_vdw_refined
X-RAY DIFFRACTION
r_symmetry_vdw_other
X-RAY DIFFRACTION
r_symmetry_hbond_refined
X-RAY DIFFRACTION
r_symmetry_hbond_other
X-RAY DIFFRACTION
r_symmetry_metal_ion_refined
X-RAY DIFFRACTION
r_symmetry_metal_ion_other
X-RAY DIFFRACTION
r_mcbond_it
X-RAY DIFFRACTION
r_mcbond_other
X-RAY DIFFRACTION
r_mcangle_it
X-RAY DIFFRACTION
r_scbond_it
X-RAY DIFFRACTION
r_scangle_it
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
LS refinement shell
Resolution: 2.97→3.047 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.333
75
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Rwork
0.269
1197
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obs
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96.07 %
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