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- PDB-1a3f: PHOSPHOLIPASE A2 (PLA2) FROM NAJA NAJA VENOM -

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Basic information

Entry
Database: PDB / ID: 1a3f
TitlePHOSPHOLIPASE A2 (PLA2) FROM NAJA NAJA VENOM
ComponentsPHOSPHOLIPASE A2
KeywordsCARBOXYLIC ESTER HYDROLASE / PHOSPHOLIPASE / TRIMER / CALCIUM BINDING / ACTIVATOR SITE
Function / homology
Function and homology information


phospholipase A2 / calcium-dependent phospholipase A2 activity / arachidonate secretion / lipid catabolic process / phospholipid metabolic process / phospholipid binding / 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
Acidic phospholipase A2 2
Similarity search - Component
Biological speciesNaja naja (Indian cobra)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsSegelke, B.W. / Nguyen, D. / Chee, R. / Xuong, H.N. / Dennis, E.A.
CitationJournal: J.Mol.Biol. / Year: 1998
Title: Structures of two novel crystal forms of Naja naja naja phospholipase A2 lacking Ca2+ reveal trimeric packing.
Authors: Segelke, B.W. / Nguyen, D. / Chee, R. / Xuong, N.H. / Dennis, E.A.
History
DepositionJan 21, 1998Processing site: BNL
Revision 1.0Apr 29, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Other / Refinement description
Category: database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Revision 1.4Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PHOSPHOLIPASE A2
B: PHOSPHOLIPASE A2
C: PHOSPHOLIPASE A2


Theoretical massNumber of molelcules
Total (without water)40,0743
Polymers40,0743
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3390 Å2
ΔGint-14 kcal/mol
Surface area16380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.220, 73.480, 87.520
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
33
/ NCS ensembles :
ID
1
2
3

NCS oper:
IDCodeMatrixVector
1given(0.989962, -0.046274, -0.133546), (0.091075, -0.513694, 0.853126), (-0.10808, -0.856724, -0.504323)3.7611, 16.1484, 48.5878
2given(0.988566, 0.105218, -0.108015), (-0.039614, -0.509949, -0.859292), (-0.145495, 0.853746, -0.49995)-0.2017, 49.8843, 12.1503

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Components

#1: Protein PHOSPHOLIPASE A2


Mass: 13357.855 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Naja naja (Indian cobra) / Cellular location: VENOM SACK / References: UniProt: P15445, phospholipase A2
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: 2.67 Å3/Da / Density % sol: 53.4 %
Crystal growTemperature: 295.5 K
Details: UNBUFFERED 32.5% MONOMETHYL PEG 5K AND 0.17M SODIUM CITRATE AT 22.5 DEGREES C., temperature 295.5K
Crystal
*PLUS
Density % sol: 54 %
Crystal grow
*PLUS
Temperature: 22.5 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
132.5 %mPEG50001reservoir
20.17 Msodium citrate1reservoir

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR / Date: Jun 1, 1995
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→72.5 Å / Num. obs: 12166 / % possible obs: 79 % / Observed criterion σ(I): 2 / Redundancy: 2.5 % / Biso Wilson estimate: 14.7 Å2 / Rsym value: 0.064 / Net I/σ(I): 8.7
Reflection shellResolution: 2.5→2.69 Å / Redundancy: 1.4 % / Mean I/σ(I) obs: 2 / Rsym value: 0.24 / % possible all: 73
Reflection
*PLUS
Num. obs: 9506 / % possible obs: 72.4 % / Num. measured all: 27711 / Rmerge(I) obs: 0.064

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Processing

Software
NameVersionClassification
UCSDSOFTWAREdata collection
UCSDSOFTWAREdata reduction
X-PLOR3model building
X-PLOR3refinement
UCSDdata scaling
X-PLOR3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PSH

1psh


Resolution: 2.65→8 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: POST REFINEMENT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.26 1029 9.72 %RANDOM
Rwork0.21 ---
obs0.21 9506 72.4 %-
Displacement parametersBiso mean: 16.3 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å / Luzzati d res low obs: 8 Å / Luzzati sigma a obs: 0.33 Å
Refinement stepCycle: LAST / Resolution: 2.65→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2784 0 0 0 2784
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
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_deg1.69
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.2
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.49
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
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Weight position: 250

Ens-IDDom-IDNCS model detailsRms dev Biso (Å2)Rms dev position (Å)Weight Biso
11RESTRAINTS001.25
220.4470.0541
330.5120.0911
LS refinement shellResolution: 2.65→2.77 Å / Rfactor Rfree error: 0.036 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.323 81 10.7 %
Rwork0.229 674 -
obs--66.7 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PARHCSDS.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.2
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.49

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