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- PDB-3ux7: Crystal structure of a dimeric myotoxic component of the Vipera a... -

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Basic information

Entry
Database: PDB / ID: 3ux7
TitleCrystal structure of a dimeric myotoxic component of the Vipera ammodytes meridionalis venom reveals determinants of myotoxicity and membrane damaging activity
ComponentsAmmodytin L(1) isoform
KeywordsTOXIN / Snake venom / Ser49 myotoxin
Function / homology
Function and homology information


phospholipase A2 activity / arachidonic acid 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
Ammodytin L(1) isoform
Similarity search - Component
Biological speciesVipera ammodytes meridionalis (snake)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.97 Å
AuthorsGeorgieva, D. / Coronado, M. / Oberthuer, D. / Buck, F. / Duhalov, D. / Arni, R.K. / Genov, N. / Betzel, C.
CitationJournal: Mol Biosyst / Year: 2012
Title: Crystal structure of a dimeric Ser49 PLA(2)-like myotoxic component of the Vipera ammodytes meridionalis venomics reveals determinants of myotoxicity and membrane damaging activity.
Authors: Georgieva, D. / Coronado, M. / Oberthur, D. / Buck, F. / Duhalov, D. / Arni, R.K. / Betzel, C.
History
DepositionDec 4, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 25, 2012Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ammodytin L(1) isoform
B: Ammodytin L(1) isoform
C: Ammodytin L(1) isoform
D: Ammodytin L(1) isoform
E: Ammodytin L(1) isoform
F: Ammodytin L(1) isoform
G: Ammodytin L(1) isoform
H: Ammodytin L(1) isoform
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,58127
Polymers107,7568
Non-polymers1,82519
Water1,62190
1
A: Ammodytin L(1) isoform
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8545
Polymers13,4691
Non-polymers3844
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ammodytin L(1) isoform
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,6623
Polymers13,4691
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Ammodytin L(1) isoform
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,6623
Polymers13,4691
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Ammodytin L(1) isoform
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,6623
Polymers13,4691
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Ammodytin L(1) isoform
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,5662
Polymers13,4691
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Ammodytin L(1) isoform
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7584
Polymers13,4691
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: Ammodytin L(1) isoform
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7584
Polymers13,4691
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
H: Ammodytin L(1) isoform
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,6623
Polymers13,4691
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)76.966, 47.673, 126.619
Angle α, β, γ (deg.)90.00, 90.25, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Ammodytin L(1) isoform


Mass: 13469.486 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Vipera ammodytes meridionalis (snake) / References: UniProt: I1SB18*PLUS
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


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

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.16 Å3/Da / Density % sol: 42.93 %
Crystal growMethod: 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

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, Hamburg / Beamline: X13 / Wavelength: 0.8123 Å
DetectorType: MAR CCD 165 mm / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8123 Å / Relative weight: 1
ReflectionResolution: 2.95→40 Å / Num. obs: 21213

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Processing

Software
NameVersionClassification
DNAdata collection
PHASERphasing
REFMAC5.6.0117refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod 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
RfactorNum. reflection% reflectionSelection details
Rfree0.26079 972 5.1 %RANDOM
Rwork0.22439 ---
obs0.22626 17915 97.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.764 Å2
Baniso -1Baniso -2Baniso -3
1-3.77 Å2-0 Å2-0.61 Å2
2---1.71 Å20 Å2
3----2.07 Å2
Refinement stepCycle: LAST / Resolution: 2.97→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7463 0 95 90 7648
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.027728
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2791.97310398
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8765968
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.62224.153301
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.532151360
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0671524
X-RAY DIFFRACTIONr_chiral_restr0.0850.21071
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0215684
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.97→3.047 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 75 -
Rwork0.269 1197 -
obs--96.07 %

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