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- PDB-6al3: Lys49 PLA2 BPII derived from the venom of Protobothrops flavoviridis. -

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Basic information

Entry
Database: PDB / ID: 6al3
TitleLys49 PLA2 BPII derived from the venom of Protobothrops flavoviridis.
ComponentsBasic phospholipase A2 BP-II
KeywordsTOXIN / Phospholipase A2 / toxic components / nake venom
Function / homology
Function and homology information


phospholipase A2 activity => GO:0004623 / phospholipase A2 activity => GO:0004623 / phospholipase A2 / phospholipase A2 activity / arachidonic acid secretion / phospholipid metabolic process / lipid catabolic process / toxin activity / calcium ion binding / extracellular region
Similarity search - Function
Phospholipase A2, aspartic acid active site / Phospholipase A2 aspartic acid active site. / Phospholipase A2, histidine active site / Phospholipase A2 histidine active site. / Phospholipase A2 / Phospholipase A2 domain / Phospholipase A2 / Phospholipase A2 / Phospholipase A2 / Phospholipase A2 domain ...Phospholipase A2, aspartic acid active site / Phospholipase A2 aspartic acid active site. / Phospholipase A2, histidine active site / Phospholipase A2 histidine active site. / Phospholipase A2 / Phospholipase A2 domain / Phospholipase A2 / Phospholipase A2 / Phospholipase A2 / Phospholipase A2 domain / Phospholipase A2 domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Basic phospholipase A2 BP-II
Similarity search - Component
Biological speciesProtobothrops flavoviridis (habu)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.57 Å
AuthorsMatsui, T. / Kamata, S. / Suzuki, A. / Oda-Ueda, N. / Ogawa, T. / Tanaka, Y.
CitationJournal: Sci Rep / Year: 2019
Title: SDS-induced oligomerization of Lys49-phospholipase A2from snake venom.
Authors: Matsui, T. / Kamata, S. / Ishii, K. / Maruno, T. / Ghanem, N. / Uchiyama, S. / Kato, K. / Suzuki, A. / Oda-Ueda, N. / Ogawa, T. / Tanaka, Y.
History
DepositionSep 5, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 16, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 27, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.pdbx_database_id_DOI
Revision 1.2Mar 6, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.3Nov 22, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Basic phospholipase A2 BP-II
B: Basic phospholipase A2 BP-II
C: Basic phospholipase A2 BP-II
D: Basic phospholipase A2 BP-II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,4457
Polymers55,1574
Non-polymers2883
Water0
1
A: Basic phospholipase A2 BP-II


Theoretical massNumber of molelcules
Total (without water)13,7891
Polymers13,7891
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Basic phospholipase A2 BP-II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9813
Polymers13,7891
Non-polymers1922
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Basic phospholipase A2 BP-II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8852
Polymers13,7891
Non-polymers961
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Basic phospholipase A2 BP-II


Theoretical massNumber of molelcules
Total (without water)13,7891
Polymers13,7891
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)126.900, 126.900, 64.880
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number172
Space group name H-MP64
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
31chain C
41chain D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: CYS / End label comp-ID: CYS / Auth seq-ID: 1 - 122 / Label seq-ID: 1 - 122

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain AAA
2chain BBB
3chain CCC
4chain DDD

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Components

#1: Protein
Basic phospholipase A2 BP-II / svPLA2 / Basic protein II / BPII / Phosphatidylcholine 2-acylhydrolase


Mass: 13789.205 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Protobothrops flavoviridis (habu) / References: UniProt: P0DJJ9, phospholipase A2
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4

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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: 2.73 Å3/Da / Density % sol: 55.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 100 mM Sodium acetate pH 4.2, 0.5 M Ammonium acetate, 32.5% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 11, 2017
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
Reflection twinOperator: h,-h-k,-l / Fraction: 0.49
ReflectionResolution: 2.57→45.363 Å / Num. obs: 19245 / % possible obs: 99.9 % / Redundancy: 6.736 % / CC1/2: 1 / Rmerge(I) obs: 0.123 / Rrim(I) all: 0.134 / Χ2: 1.156 / Net I/σ(I): 12.62 / Num. measured all: 129632
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.57-2.726.8730.564321169308730800.8460.61199.8
2.72-2.916.7680.4074.3219703291129110.8660.441100
2.91-3.146.7260.2756.4418121269426940.990.298100
3.14-3.446.9180.17910.1117199248724860.9750.194100
3.44-3.846.5670.12314.4514914227122710.9910.134100
3.84-4.436.8520.08722.1813601198619850.9960.09499.9
4.43-5.416.5810.07524.4211240170817080.9970.081100
5.41-7.66.550.06725.018711133213300.9980.07399.8
7.6-45.3636.3770.03334.31497478678010.03599.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.517
Highest resolutionLowest resolution
Rotation45.37 Å2.69 Å

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
PHENIX1.13_2998refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5VFH

5vfh


Resolution: 2.57→45.363 Å / Cross valid method: THROUGHOUT / σ(F): 1.9 / Phase error: 24.45
RfactorNum. reflection% reflection
Rfree0.2451 962 5 %
Rwork0.218 --
obs0.2269 19239 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 117.14 Å2 / Biso mean: 42.9785 Å2 / Biso min: 30.26 Å2
Refinement stepCycle: final / Resolution: 2.57→45.363 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3820 0 15 0 3835
Biso mean--45.77 --
Num. residues----488
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2401X-RAY DIFFRACTION11.611TORSIONAL
12B2401X-RAY DIFFRACTION11.611TORSIONAL
13C2401X-RAY DIFFRACTION11.611TORSIONAL
14D2401X-RAY DIFFRACTION11.611TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7 / % reflection obs: 95 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.5673-2.70260.30711380.262326132751
2.7026-2.87190.28221350.237425662701
2.8719-3.09360.26181370.229126102747
3.0936-3.40480.26221370.222425902727
3.4048-3.89710.25151360.212325852721
3.8971-4.90880.22861380.196626352773
4.9088-41.93690.24921410.2526612802

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