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- PDB-1zlb: Crystal structure of catalytically-active phospholipase A2 in the... -

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Basic information

Entry
Database: PDB / ID: 1zlb
TitleCrystal structure of catalytically-active phospholipase A2 in the absence of calcium
Componentshypotensive phospholipase A2
KeywordsHYDROLASE / Asp49-PLA2 / toxin / snake venom
Function / homology
Function and homology information


phospholipase A2 activity / phospholipase A2 / arachidonic acid secretion / phospholipid metabolic process / lipid catabolic process / regulation of blood pressure / toxin activity / defense response to bacterium / 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 BthA-1
Similarity search - Component
Biological speciesBothrops jararacussu (jararacussu)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.97 Å
AuthorsMurakami, M.T. / Cintra, A.C. / Gabdoulkhakov, A. / Genov, N. / Betzel, C. / Arni, R.K.
Citation
Journal: Biochimie / Year: 2006
Title: Insights into metal ion binding in phospholipases A(2): ultra high-resolution crystal structures of an acidic phospholipase A(2) in the Ca(2+) free and bound states.
Authors: Murakami, M.T. / Gabdoulkhakov, A. / Genov, N. / Cintra, A.C. / Betzel, C. / Arni, R.K.
#1: Journal: Biochim.Biophys.Acta / Year: 2004
Title: Crystallization and high-resolution X-ray diffraction data collection of an Asp49 PLA2 from Bothrops jararacussu venom both in the presence and absence of Ca2+ ions.
Authors: Murakami, M.T. / Michelan-Duarte, S. / Cintra, A.C.O. / Arni, R.K.
History
DepositionMay 5, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 25, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: hypotensive phospholipase A2


Theoretical massNumber of molelcules
Total (without water)13,6981
Polymers13,6981
Non-polymers00
Water4,666259
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.964, 53.794, 89.816
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-195-

HOH

21A-331-

HOH

31A-348-

HOH

41A-349-

HOH

51A-358-

HOH

61A-373-

HOH

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Components

#1: Protein hypotensive phospholipase A2


Mass: 13698.481 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: venom / Source: (natural) Bothrops jararacussu (jararacussu) / References: UniProt: Q8AXY1, phospholipase A2
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 259 / 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: 1.52 Å3/Da / Density % sol: 19.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG 3350, NaCl, EDTA, tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, Hamburg / Beamline: X11 / Wavelength: 0.8 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 14, 2004
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 0.97→10 Å / Num. all: 57413 / Num. obs: 57413 / % possible obs: 99.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.068
Reflection shellResolution: 0.97→0.99 Å / Rmerge(I) obs: 0.477 / % possible all: 97.8

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Processing

Software
NameClassification
SHELXmodel building
SHELXL-97refinement
MAR345data collection
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 0.97→10 Å / Num. parameters: 11031 / Num. restraintsaints: 13026 / σ(F): 0 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.1961 1731 -RANDOM
Rwork0.1507 ---
all0.171 ---
obs0.168 57413 95.7 %-
Refine analyzeNum. disordered residues: 5 / Occupancy sum hydrogen: 810.2 / Occupancy sum non hydrogen: 1160.4
Refinement stepCycle: LAST / Resolution: 0.97→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms969 0 0 259 1228
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.017
X-RAY DIFFRACTIONs_angle_d0.04
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0307
X-RAY DIFFRACTIONs_zero_chiral_vol0.102
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.092
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.039
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.006
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.046
X-RAY DIFFRACTIONs_approx_iso_adps0.091

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