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- PDB-1ozy: Crystal Structure of Phospholipase A2 (MIPLA3) From Micropechis I... -

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Basic information

Entry
Database: PDB / ID: 1ozy
TitleCrystal Structure of Phospholipase A2 (MIPLA3) 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: 2.7 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.D. / Luo, R.H. / Selvanayagam, Z.E. / Gopalakrishnakone, P.
History
DepositionApr 10, 2003Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 28, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 16, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3254
Polymers27,1332
Non-polymers1922
Water1,63991
1
A: PHOSPHOLIPASE A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7593
Polymers13,5671
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: PHOSPHOLIPASE A2


Theoretical massNumber of molelcules
Total (without water)13,5671
Polymers13,5671
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
A: PHOSPHOLIPASE A2
hetero molecules

B: PHOSPHOLIPASE A2


Theoretical massNumber of molelcules
Total (without water)27,3254
Polymers27,1332
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_564y,-x+1,z-1/41
Buried area1560 Å2
ΔGint-41 kcal/mol
Surface area13670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.522, 53.522, 148.272
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein PHOSPHOLIPASE A2 / MIPLA3


Mass: 13566.533 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Micropechis ikaheka (cobra) / References: phospholipase A2
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 3.83 Å3/Da / Density % sol: 67.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: ammonium sulphate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.99 / Wavelength: 0.99 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 27, 2002
RadiationMonochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 2.7→100 Å / Num. obs: 11335 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 6.8 % / Rsym value: 0.086 / Net I/σ(I): -3
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 4.8 % / Rsym value: 0.307 / % possible all: 88.2

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Processing

Software
NameVersionClassification
DENZO1.96data reduction
SCALEPACK1.96data scaling
MOLREPphasing
CNS1.1refinement
RefinementMethod to determine structure: molecular replacement
Starting model: PDB CODE: 1UNE

1une


Resolution: 2.7→8 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 155653.55 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 3
Details: TWINNING OPERATOR= h,-k,-l TWINNING FRACTION= 0.474
RfactorNum. reflection% reflectionSelection details
Rfree0.2833 862 7.8 %RANDOM
Rwork0.2276 ---
obs0.2276 9497 86.36 %-
Solvent computationSolvent model: FLAT MODEL
Displacement parametersBiso mean: 51.9541 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error free: 0.47 Å / Luzzati sigma a free: 0.8 Å
Refinement stepCycle: LAST / Resolution: 2.7→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1880 0 10 91 1981
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
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_deg1.825
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.44
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.96
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.821.5
X-RAY DIFFRACTIONc_mcangle_it2.532
X-RAY DIFFRACTIONc_scbond_it3.262
X-RAY DIFFRACTIONc_scangle_it4.152.5
LS refinement shellResolution: 2.7→2.79 Å / Rfactor Rfree error: 0.005 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.3144 41 3.78 %
Rwork0.3277 481 -
obs--48 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP

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