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- PDB-2qhe: Crystal structure of Ser49-PLA2 (ecarpholin S) from Echis carinat... -

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Basic information

Entry
Database: PDB / ID: 2qhe
TitleCrystal structure of Ser49-PLA2 (ecarpholin S) from Echis carinatus sochureki snake venom
ComponentsPhospholipase A2
KeywordsHYDROLASE / BETA SHEET / THREE HELICES
Function / homology
Function and homology information


calcium-dependent phospholipase A2 activity / arachidonic acid secretion / phospholipid metabolic process / lipid catabolic process / negative regulation of T cell proliferation / 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, 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
Basic phospholipase A2 homolog ecarpholin S
Similarity search - Component
Biological speciesEchis carinatus (saw-scaled viper)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsZhou, X. / Valiyaveettil, S. / Go, M.L. / Kini, R.M. / Sivaraman, J.
CitationJournal: Biophys.J. / Year: 2008
Title: Structural Characterization of Myotoxic Ecarpholin S from Echis carinatus Venom
Authors: Zhou, X. / Tan, T.C. / Valiyaveettil, S. / Go, M.L. / Kini, R.M. / Velazquez-Campoy, A. / Sivaraman, J.
History
DepositionJul 2, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 16, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Oct 25, 2023Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phospholipase A2


Theoretical massNumber of molelcules
Total (without water)13,8391
Polymers13,8391
Non-polymers00
Water1,72996
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.231, 39.487, 68.942
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Phospholipase A2 / / Ecarpholin S / Phosphatidylcholine 2-acylhydrolase


Mass: 13838.879 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: snake venom gland / Source: (natural) Echis carinatus (saw-scaled viper) / References: UniProt: P48650, phospholipase A2
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 96 / 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: 1.68 Å3/Da / Density % sol: 26.9 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 5.6
Details: 20% PEG3350, 20% iso-propanol, 0.1M sodium citrate pH5.6, EVAPORATION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 10, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 6463 / % possible obs: 95.7 % / Redundancy: 5 % / Rmerge(I) obs: 0.051 / Χ2: 1.014 / Net I/σ(I): 30.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2-2.074.70.145751.02987.4
2.07-2.154.90.116581.04199.7
2.15-2.255.10.0986451.04798.2
2.25-2.375.10.0866301.01197.2
2.37-2.525.10.0756430.98997
2.52-2.715.10.0626611.00498.5
2.71-2.9950.0536551.04497.5
2.99-3.425.10.0466510.99895.6
3.42-4.315.10.0416691.03596
4.31-504.90.0476760.94990.5

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
PDB_EXTRACT2data extraction
CrystalCleardata collection
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1JIA

1jia


Resolution: 2→20 Å / FOM work R set: 0.848 / σ(F): 110
RfactorNum. reflection% reflection
Rfree0.255 611 9.1 %
Rwork0.192 --
obs-6322 94.3 %
Solvent computationBsol: 92.951 Å2
Displacement parametersBiso mean: 30.548 Å2
Baniso -1Baniso -2Baniso -3
1-0.038 Å20 Å20 Å2
2---0.108 Å20 Å2
3---0.069 Å2
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms959 0 0 96 1055
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.258
X-RAY DIFFRACTIONc_mcbond_it1.1991.5
X-RAY DIFFRACTIONc_scbond_it1.9442
X-RAY DIFFRACTIONc_mcangle_it1.7152
X-RAY DIFFRACTIONc_scangle_it2.7242.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
2-2.060.196441
2.06-2.130.217180.188504522
2.13-2.20.234730.19464537
2.2-2.290.265640.2456520
2.29-2.390.306610.197458519
2.39-2.520.286680.223449517
2.52-2.680.199430.178491534
2.68-2.880.287540.189492546
2.88-3.170.277620.202468530
3.17-3.630.246530.172486539
3.63-4.560.276550.185493548
4.56-200.216600.204509569
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top

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