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- PDB-1god: MONOMERIC LYS-49 PHOSPHOLIPASE A2 HOMOLOGUE ISOLATED FROM THE VEN... -

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Basic information

Entry
Database: PDB / ID: 1god
TitleMONOMERIC LYS-49 PHOSPHOLIPASE A2 HOMOLOGUE ISOLATED FROM THE VENOM OF CERROPHIDION (BOTHROPS) GODMANI
ComponentsPROTEIN (PHOSPHOLIPASE A2)
KeywordsHYDROLASE / LYS49-PHOSPHOLIPASE A2 / SNAKE VENOM / BOTHROPS
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 GodMT-II
Similarity search - Component
Biological speciesCerrophidion godmani (Godman's montane pit viper)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsArni, R.K. / Fontes, M.R.M. / Barberato, C. / Gutierrez, J.M. / Diaz-Oreiro, C. / Ward, R.J.
Citation
Journal: Arch.Biochem.Biophys. / Year: 1999
Title: Crystal structure of myotoxin II, a monomeric Lys49-phospholipase A2 homologue isolated from the venom of Cerrophidion (Bothrops) godmani.
Authors: Arni, R.K. / Fontes, M.R. / Barberato, C. / Gutierrez, J.M. / Diaz, C. / Ward, R.J.
#1: Journal: Protein Pept.Lett. / Year: 1998
Title: Crystallization and Preliminary X-Ray Diffraction Analysis of a Lys49-Pla2 Homologue from Cerrophidion Godmani Venom
Authors: De Azevedo Jr., W.F. / Ward, R.J. / Gutierrez, J.M. / Diaz-Oreiro, C. / Arni, R.K.
History
DepositionApr 16, 1999Deposition site: RCSB / Processing site: NDB
Revision 1.0Apr 23, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Refinement description / Category: database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (PHOSPHOLIPASE A2)


Theoretical massNumber of molelcules
Total (without water)13,7341
Polymers13,7341
Non-polymers00
Water90150
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.560, 60.560, 84.720
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Cell settingtetragonal
Space group name H-MP43212

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Components

#1: Protein PROTEIN (PHOSPHOLIPASE A2) / EC 3.1.1.4 / GODMT-II


Mass: 13733.950 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Cerrophidion godmani (Godman's montane pit viper)
References: UniProt: P81165, phospholipase A2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / 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: 2.8 Å3/Da / Density % sol: 59 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 4.6
Details: 0.1 M SODIUM ACETATE (PH 4.6), 2.0 M (NH4)2SO4, 1MM NANO3, VAPOR DIFFUSION, HANGING DROP
Crystal
*PLUS
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
15 mg/mlprotein1drop
20.1 Macetate1reservoirpH4.6
32.0 Mammonium sulfate1reservoir
41 mM1reservoirNaN3

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Jan 15, 1995
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→8 Å / Num. obs: 22540 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 3 % / Rsym value: 0.09
Reflection
*PLUS
Num. obs: 4482 / Num. measured all: 22540 / Rmerge(I) obs: 0.09

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLOR3.851refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1CLP

1clp


Resolution: 2.8→8 Å / Rfactor Rfree error: 0.016 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.282 327 10.5 %RANDOM
Rwork0.188 ---
obs-3129 78.1 %-
Displacement parametersBiso mean: 35.5 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.53 Å0.35 Å
Refinement stepCycle: LAST / Resolution: 2.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms949 0 0 50 999
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.015
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.6
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.2
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.22
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.8→2.97 Å / Rfactor Rfree error: 0.068 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.36 37 11.4 %
Rwork0.23 288 -
obs--50.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 8 Å / σ(F): 2 / % reflection Rfree: 10.5 % / Rfactor obs: 0.188
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 35.5 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.6
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.2
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.22
LS refinement shell
*PLUS
Highest resolution: 2.8 Å / Rfactor Rfree: 0.36 / % reflection Rfree: 11.4 % / Rfactor Rwork: 0.23

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