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- PDB-3dih: Crystal structure of ammodytin L -

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Basic information

Entry
Database: PDB / ID: 3dih
TitleCrystal structure of ammodytin L
ComponentsPhospholipase A2 homolog, ammodytin L
KeywordsTOXIN / phospholipase A2 fold / Myotoxin / Secreted
Function / homology
Function and homology information


phospholipase A2 activity / arachidonic acid secretion / phospholipid metabolic process / lipid catabolic process / toxin activity / 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 ammodytin L
Similarity search - Component
Biological speciesVipera ammodytes ammodytes (western sand viper)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsTurk, D. / Guncar, G. / Krizaj, I.
CitationJournal: To be Published
Title: Crystal structure of ammodytin L
Authors: Turk, D. / Guncar, G. / Krizaj, I.
History
DepositionJun 20, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 5, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phospholipase A2 homolog, ammodytin L


Theoretical massNumber of molelcules
Total (without water)13,8971
Polymers13,8971
Non-polymers00
Water1,874104
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Phospholipase A2 homolog, ammodytin L

A: Phospholipase A2 homolog, ammodytin L


Theoretical massNumber of molelcules
Total (without water)27,7942
Polymers27,7942
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation18_654-x+4/3,-x+y+2/3,-z-1/31
Buried area1600 Å2
ΔGint-19 kcal/mol
Surface area12980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.500, 120.500, 63.150
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Detailsthis can sometimes form a homodimer, but the depositors don't know what is biologically active form.

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Components

#1: Protein Phospholipase A2 homolog, ammodytin L


Mass: 13897.074 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Vipera ammodytes ammodytes (western sand viper)
References: UniProt: P17935
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 104 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE 55TH RESIDUE IS SER IN THIS ENTRY AGAINST PRO IN PA2L_VIPAA. THIS IS A MINOR VARIANT.

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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: 3.17 Å3/Da / Density % sol: 61.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 0.2M glycine, pH 9, 1M NaCl, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: ENRAF-NONIUS FAST / Detector: AREA DETECTOR / Date: Aug 17, 1994
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→22.8 Å / Num. all: 5349 / Num. obs: 5349 / % possible obs: 96.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Biso Wilson estimate: 38 Å2 / Rsym value: 0.09 / Net I/σ(I): 7.7
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 5.9 % / Mean I/σ(I) obs: 2.8 / Num. unique all: 498 / Rsym value: 0.268 / % possible all: 94.4

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Processing

Software
NameClassification
AMoREphasing
MAINrefinement
MOSFLMdata reduction
rotavata/agrovatadata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→21.34 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.226 256 random
Rwork0.156 --
all0.159 5349 -
obs0.159 5323 -
Displacement parametersBiso mean: 27.3 Å2
Baniso -1Baniso -2Baniso -3
1--0.31 Å20.26 Å20 Å2
2---0.31 Å20 Å2
3---0.62 Å2
Refinement stepCycle: LAST / Resolution: 2.6→21.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms963 0 0 104 1067
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.19
X-RAY DIFFRACTIONo_bond_d_na
X-RAY DIFFRACTIONo_bond_d_prot
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_d_na
X-RAY DIFFRACTIONo_angle_d_prot
X-RAY DIFFRACTIONo_angle_deg2
X-RAY DIFFRACTIONo_angle_deg_na
X-RAY DIFFRACTIONo_angle_deg_prot
X-RAY DIFFRACTIONo_dihedral_angle_d
X-RAY DIFFRACTIONo_dihedral_angle_d_na
X-RAY DIFFRACTIONo_dihedral_angle_d_prot
X-RAY DIFFRACTIONo_improper_angle_d
X-RAY DIFFRACTIONo_improper_angle_d_na
X-RAY DIFFRACTIONo_improper_angle_d_prot
X-RAY DIFFRACTIONo_mcbond_it
X-RAY DIFFRACTIONo_mcangle_it
X-RAY DIFFRACTIONo_scbond_it
X-RAY DIFFRACTIONo_scangle_it
LS refinement shellResolution: 2.6→2.69 Å /
RfactorNum. reflection
Rfree0.268 23
Rwork0.185 -
obs-493

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