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- PDB-1b4w: BASIC PHOSPHOLIPASE A2 FROM AGKISTRODON HALYS PALLAS-IMPLICATIONS... -

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Basic information

Entry
Database: PDB / ID: 1b4w
TitleBASIC PHOSPHOLIPASE A2 FROM AGKISTRODON HALYS PALLAS-IMPLICATIONS FOR ITS ASSOCIATION AND ANTICOAGULANT ACTIVITIES BY X-RAY CRYSTALLOGRAPHY
ComponentsPROTEIN (PHOSPHOLIPASE A2)
KeywordsHYDROLASE / BASIC PHOSPHOLIPASE A2 / AGKISTRODON HALYS PALLAS / DIMER / ANTICOAGULANT ACTIVITY
Function / homology
Function and homology information


phospholipase A2 / calcium-dependent phospholipase A2 activity / arachidonate secretion / lipid catabolic process / negative regulation of T cell proliferation / phospholipid metabolic process / 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 / Phospholipase A2, histidine active site / Phospholipase A2 histidine active site. / 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 / Phospholipase A2, histidine active site / Phospholipase A2 histidine active site. / 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 B
Similarity search - Component
Biological speciesGloydius halys (Halys viper)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsZhao, K.H. / Lin, Z.J.
Citation
Journal: Toxicon / Year: 2000
Title: Structure of basic phospholipase A2 from Agkistrodon halys Pallas: implications for its association, hemolytic and anticoagulant activities.
Authors: Zhao, K. / Zhou, Y. / Lin, Z.
#1: Journal: SCI.CHINA, SER.C: LIFE SCI. / Year: 1999
Title: Refined Structure of Basic Phospholipase A2 from the Venom of Agkistrodon Halys Pallas in Orthorhombic Crystal Form I at 0.25Nm Resolution (in: C)
Authors: Zhao, K.H. / Song, S.Y. / Lin, Z.J. / Zhou, Y.C.
History
DepositionDec 30, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Jan 12, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Nov 3, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.6Aug 9, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.7Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (PHOSPHOLIPASE A2)
B: PROTEIN (PHOSPHOLIPASE A2)
C: PROTEIN (PHOSPHOLIPASE A2)
D: PROTEIN (PHOSPHOLIPASE A2)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,2776
Polymers55,6934
Non-polymers5852
Water1,946108
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.453, 54.294, 108.388
Angle α, β, γ (deg.)90.00, 111.76, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.32541, -0.82485, 0.46232), (-0.82888, 0.01354, -0.55926), (0.45504, -0.5652, -0.6881)33.87759, 37.4112, 18.50869
2given(0.4819, 0.82124, -0.3055), (0.84472, -0.52808, -0.08711), (-0.23287, -0.21608, -0.9482)27.87276, -40.66035, 52.32435
3given(-0.97411, -0.01573, -0.22552), (-0.18562, -0.51379, 0.8376), (-0.12905, 0.85777, 0.49757)81.2571, -19.51758, 22.54129
4given(-0.59617, -0.64133, 0.48298), (-0.67408, 0.07305, -0.73504), (0.43612, -0.76378, -0.47586)50.52106, 39.11212, 10.08955
5given(-0.96295, -0.25444, -0.08939), (0.07215, -0.56242, 0.8237), (-0.25986, 0.78673, 0.55994)76.71654, -28.98952, 23.42872
6given(0.41212, 0.87391, -0.25774), (0.82131, -0.47879, -0.31017), (-0.39446, -0.08386, -0.91508)36.10636, -31.96317, 56.36183

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Components

#1: Protein
PROTEIN (PHOSPHOLIPASE A2) / PLA2


Mass: 13923.168 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Gloydius halys (Halys viper) / Cellular location: EXTRACELLULAR / Secretion: YES / References: UniProt: O42187, phospholipase A2
#2: Sugar ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / 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: 2.45 Å3/Da / Density % sol: 50 %
Description: THE STRUCTURE OF BASIC PLA2 FROM AGKISTRODON HALYS PALLAS IN C2 CRYSTAL FORM WAS DETERMINED BY MOLECULAR REPLACEMENT METHOD, USING A CHAIN STRUCTURE OF THE SAME ENZYME IN P212121 CRYSTAL ...Description: THE STRUCTURE OF BASIC PLA2 FROM AGKISTRODON HALYS PALLAS IN C2 CRYSTAL FORM WAS DETERMINED BY MOLECULAR REPLACEMENT METHOD, USING A CHAIN STRUCTURE OF THE SAME ENZYME IN P212121 CRYSTAL FORM (PDB CODE 1JIA) AS SEARCH MODEL.
Crystal growpH: 8.5
Details: THE PROTEIN SOLUTIONS CONTAINED 0.1M LI2SO4, 9% PEG 4K AND 0.3% N-OCTYL BETA- D-GLUCOPYRANOSIDE IN 0.01M TRIS-HCL BUFFER(PH 8.5) AND AN ENZYME CONCENTRATION OF 8MG/ML; THE SOLUTION IN ...Details: THE PROTEIN SOLUTIONS CONTAINED 0.1M LI2SO4, 9% PEG 4K AND 0.3% N-OCTYL BETA- D-GLUCOPYRANOSIDE IN 0.01M TRIS-HCL BUFFER(PH 8.5) AND AN ENZYME CONCENTRATION OF 8MG/ML; THE SOLUTION IN RESERVOIR CONTAINED 18% PEG 4K IN SAME BUFFER, ROOM TEMPERATURE OF 17DEG.C.
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
18 mg/mlprotein1drop
28 %(w/v)PEG40001drop
30.1 MTris-HCl1drop
40.1 M1dropLi2SO4
50.3 %beta-OG1drop
616 %(v/v)PEG40001reservoir

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Data collection

DiffractionMean temperature: 280 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Aug 15, 1997
RadiationMonochromator: NICKEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 16462 / % possible obs: 97.3 % / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Biso Wilson estimate: 38 Å2 / Rmerge(I) obs: 0.102 / Rsym value: 0.087 / Net I/σ(I): 10.4
Reflection shellResolution: 2.6→2.8 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.381 / Mean I/σ(I) obs: 2.6 / Rsym value: 0.368 / % possible all: 96.3
Reflection
*PLUS
Lowest resolution: 50 Å / Num. measured all: 42427
Reflection shell
*PLUS
% possible obs: 93.1 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLOR3.8refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PP2

1pp2


Resolution: 2.6→8 Å / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.286 1570 9.63 %RANDOM
Rwork0.205 ---
obs0.205 15641 95.9 %-
Displacement parametersBiso mean: 25.9 Å2
Refine analyzeLuzzati coordinate error obs: 0.26 Å / Luzzati d res low obs: 6 Å
Refinement stepCycle: LAST / Resolution: 2.6→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3856 0 40 108 4004
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.17
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.2
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.59
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCSNCS model details: RESTRAINTS
LS refinement shellResolution: 2.6→2.71 Å / Total num. of bins used: 1
RfactorNum. reflection% reflection
Rfree0.387 166 10.6 %
Rwork0.314 1712 -
obs--93.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19X.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM.WATTOPH1919.SOL
X-RAY DIFFRACTION3PARAM3.CHOTOPH3.CHO
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refinement
*PLUS
σ(F): 2 / % reflection Rfree: 9.63 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 25.9 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.2
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.59
LS refinement shell
*PLUS
Rfactor Rfree: 0.387 / % reflection Rfree: 10.6 % / Rfactor Rwork: 0.314

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