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- PDB-1pwo: Crystal Structure of Phospholipase A2 (MIPLA2) from Micropechis I... -

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Basic information

Entry
Database: PDB / ID: 1pwo
TitleCrystal Structure of Phospholipase A2 (MIPLA2) from Micropechis Ikaheka
ComponentsPhospholipase A2
KeywordsHYDROLASE / Phospholipase A2 / Micropechis Ikaheka / Pancreatic Loop
Function / homologyPhospholipase A2 / Phospholipase A2 domain / Up-down Bundle / Mainly Alpha
Function and homology information
Biological speciesMicropechis ikaheka (cobra)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsLok, S.M. / Swaminathan, K.
Citation
Journal: Febs J. / Year: 2005
Title: Structure and function comparison of Micropechis ikaheka snake venom phospholipase A2 isoenzymes.
Authors: Lok, S.M. / Gao, R. / Rouault, M. / Lambeau, G. / Gopalakrishnakone, P. / Swaminathan, K.
#1: Journal: BIOCHIM.BIOPHYS.ACTA / Year: 2001
Title: Purification and properties of three new phospholipase A2 isoenzymes from Micropechis ikaheka venom.
Authors: Gao, R. / Kini, R.M. / Li, G. / Luo, R. / Selvanayagam, Z.E. / Gopalakrishnakone, P.
History
DepositionJul 2, 2003Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 1, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 3, 2024Group: 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 1.4Nov 6, 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: Phospholipase A2
B: Phospholipase A2
C: Phospholipase A2
D: Phospholipase A2


Theoretical massNumber of molelcules
Total (without water)55,9324
Polymers55,9324
Non-polymers00
Water5,783321
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)129.186, 100.643, 88.307
Angle α, β, γ (deg.)90.00, 133.17, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Phospholipase A2 / MIPLA2


Mass: 13983.006 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Micropechis ikaheka (cobra) / Secretion: venom / References: phospholipase A2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 321 / 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: 3.57 Å3/Da / Density % sol: 65.24 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.6
Details: 2.4M Ammonium Sulphate, pH 6.6, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Jan 1, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 25377 / Num. obs: 22385 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Redundancy: 1.3 % / Biso Wilson estimate: 37.6 Å2 / Rsym value: 0.054
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 1.3 % / Mean I/σ(I) obs: 4.52 / Num. unique all: 2491 / Rsym value: 0.211 / % possible all: 99.2

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: MiPLA4

Resolution: 2.6→8 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 540537.68 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 3
RfactorNum. reflection% reflectionSelection details
Rfree0.271 2107 9.7 %RANDOM
Rwork0.226 ---
obs0.226 21722 88.6 %-
all-53788 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 62.7729 Å2 / ksol: 0.486051 e/Å3
Displacement parametersBiso mean: 40.8 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.44 Å0.36 Å
Refinement stepCycle: LAST / Resolution: 2.6→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3872 0 0 321 4193
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.9
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.12
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.34 214 7.5 %
Rwork0.293 2657 -
obs--70.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER_REP.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4GLYCEROL.PARAMGLYCEROL.TOP

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