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- PDB-1oz6: X-ray structure of acidic phospholipase A2 from Indian saw-scaled... -

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Basic information

Entry
Database: PDB / ID: 1oz6
TitleX-ray structure of acidic phospholipase A2 from Indian saw-scaled viper (Echis carinatus) with a potent platelet aggregation inhibitory activity
Componentsphospholipase A2
KeywordsHYDROLASE / enzyme / PLA2
Function / homology
Function and homology information


phospholipase A2 activity => GO:0004623 / phospholipase A2 activity => GO:0004623 / phospholipase A2 activity / phospholipase A2 / 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
Acidic phospholipase A2 EC-I
Similarity search - Component
Biological speciesEchis carinatus (saw-scaled viper)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsJasti, J. / Paramasivam, M. / Srinivasan, A. / Singh, T.P.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2004
Title: Structure of an acidic phospholipase A2 from Indian saw-scaled viper (Echis carinatus) at 2.6 A resolution reveals a novel intermolecular interaction.
Authors: Jasti, J. / Paramasivam, M. / Srinivasan, A. / Singh, T.P.
History
DepositionApr 8, 2003Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 30, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: phospholipase A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7682
Polymers13,7281
Non-polymers401
Water1,62190
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.963, 57.876, 33.682
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein phospholipase A2 /


Mass: 13727.504 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Echis carinatus (saw-scaled viper) / Secretion: venom / References: UniProt: Q7T3S7, phospholipase A2
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#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: 2.14 Å3/Da / Density % sol: 41.99 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 50mM Ammonium acetate, 10mM Calcium chloride, 55% ethanol, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 283 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 12, 2002 / Details: mirrors
RadiationMonochromator: osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→20 Å / Num. all: 3944 / Num. obs: 3944 / % possible obs: 97 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 11 % / Biso Wilson estimate: 42.4 Å2 / Rmerge(I) obs: 0.098 / Rsym value: 0.098 / Net I/σ(I): 11
Reflection shellResolution: 2.6→2.66 Å / Redundancy: 4 % / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 2.3 / Num. unique all: 144 / Rsym value: 0.23 / % possible all: 91

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Processing

Software
NameVersionClassification
REFMAC5refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1cl5

1cl5


Resolution: 2.6→20 Å / Rfactor Rfree error: 0.02 / Data cutoff high absF: 855787.47 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.257 208 5.3 %RANDOM
Rwork0.192 ---
all0.211 3375 --
obs0.207 3375 95.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 48.3827 Å2 / ksol: 0.29832 e/Å3
Displacement parametersBiso mean: 33.9 Å2
Baniso -1Baniso -2Baniso -3
1-14.62 Å20 Å20 Å2
2---8.77 Å20 Å2
3----5.85 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.57 Å0.38 Å
Refinement stepCycle: LAST / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms951 0 1 90 1042
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONr_bond_d0.006
X-RAY DIFFRACTIONr_bond_d_na
X-RAY DIFFRACTIONr_bond_d_prot
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_d_na
X-RAY DIFFRACTIONr_angle_d_prot
X-RAY DIFFRACTIONr_angle_deg1.2
X-RAY DIFFRACTIONr_angle_deg_na
X-RAY DIFFRACTIONr_angle_deg_prot
X-RAY DIFFRACTIONr_dihedral_angle_d22.9
X-RAY DIFFRACTIONr_dihedral_angle_d_na
X-RAY DIFFRACTIONr_dihedral_angle_d_prot
X-RAY DIFFRACTIONr_improper_angle_d0.77
X-RAY DIFFRACTIONr_improper_angle_d_na
X-RAY DIFFRACTIONr_improper_angle_d_prot
X-RAY DIFFRACTIONr_mcbond_it1.441.5
X-RAY DIFFRACTIONr_mcangle_it2.432
X-RAY DIFFRACTIONr_scbond_it2.412
X-RAY DIFFRACTIONr_scangle_it3.762.5
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.078 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.341 31 5.4 %
Rwork0.276 542 -
obs-144 87.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMWATER.TOP
X-RAY DIFFRACTION3WATER.PARAMION.TOP

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