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- PDB-5vet: PHOSPHOLIPASE A2, RE-REFINEMENT OF THE PDB STRUCTURE 1JQ8 WITHOUT... -

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Basic information

Entry
Database: PDB / ID: 5vet
TitlePHOSPHOLIPASE A2, RE-REFINEMENT OF THE PDB STRUCTURE 1JQ8 WITHOUT THE PUTATIVE COMPLEXED OLIGOPEPTIDE
ComponentsPhospholipase A2 VRV-PL-VIIIa
KeywordsHYDROLASE / PHOSPHOLIPASE A2 / RE-REFINEMENT
Function / homology
Function and homology information


phospholipase A2 / calcium-dependent phospholipase A2 activity / arachidonate secretion / phospholipid metabolic process / lipid catabolic process / negative regulation of T cell proliferation / phospholipid binding / toxin activity / 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 VRV-PL-VIIIa / Basic phospholipase A2 VRV-PL-VIIIa
Similarity search - Component
Biological speciesDaboia russellii pulchella (snake)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsWlodawer, A. / Dauter, Z. / Minor, W. / Stanfield, R. / Porebski, P. / Jaskolski, M. / Pozharski, E. / Weichenberger, C.X. / Rupp, B.
CitationJournal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2002
Title: Design of specific peptide inhibitors of phospholipase A2: structure of a complex formed between Russell's viper phospholipase A2 and a designed peptide Leu-Ala-Ile-Tyr-Ser (LAIYS).
Authors: Chandra, V. / Jasti, J. / Kaur, P. / Dey, S. / Srinivasan, A. / Betzel, C.h. / Singh, T.P.
History
DepositionApr 5, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 20, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 13, 2022Group: Database references / Structure summary / Category: audit_author / citation_author / database_2
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 0This entry reflects an alternative modeling of the original data in 1JQ8, determined by V.CHANDRA,J. ...This entry reflects an alternative modeling of the original data in 1JQ8, determined by V.CHANDRA,J.JASTI,P.KAUR,S.DEY,C.BETZEL,T.P.SINGH
Remark 200SEE THE ORIGINAL DATA, ENTRY 1JQ8
Remark 280SEE THE ORIGINAL DATA, ENTRY 1JQ8

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phospholipase A2 VRV-PL-VIIIa
B: Phospholipase A2 VRV-PL-VIIIa


Theoretical massNumber of molelcules
Total (without water)27,2602
Polymers27,2602
Non-polymers00
Water4,828268
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: DIMER
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1340 Å2
ΔGint-14 kcal/mol
Surface area13010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.825, 90.375, 77.590
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-239-

HOH

21B-265-

HOH

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Components

#1: Protein Phospholipase A2 VRV-PL-VIIIa


Mass: 13629.767 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Daboia russellii pulchella (snake)
References: UniProt: D0VX11, UniProt: P59071*PLUS, phospholipase A2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 268 / 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: 2.47 Å3/Da / Density % sol: 50.21 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 20MM SODIUM CACODYLATE, 1.4M AMMONIUM SULFATE, 4MM CALCIUM CHLORIDE, 3% DIOXANE, PH 6.5

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Data collection

DiffractionMean temperature: 180 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.98 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 20, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2→19.51 Å / Num. obs: 17841 / % possible obs: 96.6 % / Redundancy: 12.4 % / Net I/σ(I): 43.8

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Processing

Software
NameVersionClassification
REFMACrefinement
PDB_EXTRACT3.22data extraction
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→19.51 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.94 / SU B: 5.846 / SU ML: 0.153 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.162 / ESU R Free: 0.166
RfactorNum. reflection% reflectionSelection details
Rfree0.2269 861 4.8 %RANDOM
Rwork0.1551 ---
obs0.1585 17037 96.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 130.88 Å2 / Biso mean: 41.284 Å2 / Biso min: 18.09 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å2-0 Å2
2---0.01 Å20 Å2
3----0.01 Å2
Refinement stepCycle: final / Resolution: 2→19.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1888 0 0 268 2156
Biso mean---49.28 -
Num. residues----242
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.021942
X-RAY DIFFRACTIONr_angle_refined_deg1.7871.9662614
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1915240
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.92523.90282
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.1115348
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7041510
X-RAY DIFFRACTIONr_chiral_restr0.1210.2264
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211450
LS refinement shellResolution: 2.003→2.054 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.247 62 -
Rwork0.244 1138 -
all-1200 -
obs--88.63 %

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