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- PDB-1cl5: CRYSTAL STRUCTURE OF PHOSPHOLIPASE A2 FROM DABOIA RUSSELLI PULCHELLA -

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Basic information

Entry
Database: PDB / ID: 1cl5
TitleCRYSTAL STRUCTURE OF PHOSPHOLIPASE A2 FROM DABOIA RUSSELLI PULCHELLA
ComponentsPROTEIN (PHOSPHOLIPASE A2)
KeywordsHYDROLASE / PHOSPHOLIPASE A2 / NEUROTOXIC / DABOIA RUSSELLI PULCHELLA
Function / homology
Function and homology information


phospholipase A2 / calcium-dependent phospholipase A2 activity / arachidonate secretion / lipid catabolic process / negative regulation of T cell proliferation / phospholipid metabolic process / phospholipid binding / 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 / Phospholipase A2, histidine active site / Phospholipase A2 histidine active site. / 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 / Phospholipase A2, histidine active site / Phospholipase A2 histidine active site. / 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 VRV-PL-VIIIa
Similarity search - Component
Biological speciesDaboia russellii pulchella (snake)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsChandra, V. / Kaur, P. / Singh, T.P.
Citation
Journal: J.Mol.Biol. / Year: 2000
Title: Three-dimensional structure of a presynaptic neurotoxic phospholipase A2 from Daboia russelli pulchella at 2.4 A resolution.
Authors: Chandra, V. / Kaur, P. / Srinivasan, A. / Singh, T.P.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1999
Title: Purification, crystallization and preliminary x-ray crystallographic analysis of a phospholipase A2 from Daboia russelli pulchella.
Authors: Chandra, V. / Nagpal, A. / Srinivasan, A. / Singh, T.P.
History
DepositionMay 6, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0May 12, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 27, 2019Group: Database references / Category: citation
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.4Aug 9, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (PHOSPHOLIPASE A2)
B: PROTEIN (PHOSPHOLIPASE A2)


Theoretical massNumber of molelcules
Total (without water)27,2602
Polymers27,2602
Non-polymers00
Water2,882160
1
A: PROTEIN (PHOSPHOLIPASE A2)


Theoretical massNumber of molelcules
Total (without water)13,6301
Polymers13,6301
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PROTEIN (PHOSPHOLIPASE A2)


Theoretical massNumber of molelcules
Total (without water)13,6301
Polymers13,6301
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.048, 92.347, 77.049
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein PROTEIN (PHOSPHOLIPASE A2)


Mass: 13629.767 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Daboia russellii pulchella (snake) / Secretion: VENOM / Species: Daboia russellii / Strain: pulchella / References: UniProt: P59071, phospholipase A2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 160 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.45 Å3/Da / Density % sol: 49 %
Description: THE R CHAIN OF PDB ENTRY 1PP2 WAS USED FOR MOLECULAR REPLACEMENT.
Crystal growpH: 7
Details: PROTEIN WAS CRYSTALLISED FROM 1.2 AMMONIUM SULPHATE BUFFER WITH 20MM SODIUM CACODYLATE, 2MM CALCIUM CHLORIDE AND 3% DIOXANE, pH 7.0
Crystal
*PLUS
Density % sol: 47 %
Crystal grow
*PLUS
Temperature: 298 K / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115 mg/mlprotease1drop
220 mMsodium cacodylate1drop
31 mMcalcium chloride1drop
43 %(v/v)dioxane1drop
51.2 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 283 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 1, 1998 / Details: PIN HOLE
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.45→20 Å / Num. obs: 61402 / % possible obs: 97.8 % / Observed criterion σ(I): -3 / Redundancy: 6.04 % / Biso Wilson estimate: 35 Å2 / Rmerge(I) obs: 0.098 / Rsym value: 0.098 / Net I/σ(I): 16.02
Reflection shellResolution: 2.45→2.54 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.191 / Mean I/σ(I) obs: 14.2 / Rsym value: 0.191 / % possible all: 98.4
Reflection
*PLUS
Highest resolution: 2.4 Å / Num. obs: 10169 / % possible obs: 98 % / Redundancy: 3.9 %
Reflection shell
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 2.5 Å / Rmerge(I) obs: 0.116

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLOR3.851refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PP2

1pp2


Resolution: 2.45→20 Å / Rfactor Rfree error: 0.011 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.267 541 5.3 %RANDOM
Rwork0.188 ---
obs-10169 98.7 %-
Displacement parametersBiso mean: 28.6 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.37 Å0.3 Å
Refinement stepCycle: LAST / Resolution: 2.45→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1886 0 0 160 2046
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.007
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_deg1.1
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.8
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.62
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.71.5
X-RAY DIFFRACTIONx_mcangle_it4.162
X-RAY DIFFRACTIONx_scbond_it4.22
X-RAY DIFFRACTIONx_scangle_it6.032.5
LS refinement shellResolution: 2.45→2.6 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.329 95 5.6 %
Rwork0.269 1594 -
obs--98.7 %
Xplor fileSerial no: 1 / Param file: PARHCSDX.PRO / Topol file: TOPHCSDX.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.8
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.62

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