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- PDB-1bk9: PHOSPHOLIPASE A2 MODIFIED BY PBPB -

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Basic information

Entry
Database: PDB / ID: 1bk9
TitlePHOSPHOLIPASE A2 MODIFIED BY PBPB
ComponentsPHOSPHOLIPASE A2
KeywordsHYDROLASE / PHOSPHOLIPASE A2 / PLATELET AGGREGATION INHIBITOR / PBPB
Function / homology
Function and homology information


phospholipase A2 / calcium-dependent phospholipase A2 activity / arachidonate secretion / phospholipid metabolic process / lipid catabolic 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, 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
1,4-BUTANEDIOL / p-Bromophenacyl bromide / Acidic phospholipase A2
Similarity search - Component
Biological speciesGloydius halys (Halys viper)
MethodX-RAY DIFFRACTION / DIFFERENT FOURIER / Resolution: 2 Å
AuthorsZhao, H. / Tang, L. / Wang, X. / Lin, Z. / Zhou, Y.
CitationJournal: Toxicon / Year: 1998
Title: Structure of a snake venom phospholipase A2 modified by p-bromo-phenacyl-bromide.
Authors: Zhao, H. / Tang, L. / Wang, X. / Zhou, Y. / Lin, Z.
History
DepositionJul 16, 1998Processing site: BNL
Revision 1.0Mar 2, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Nov 27, 2019Group: Advisory / Derived calculations ...Advisory / Derived calculations / Experimental preparation / Non-polymer description / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / exptl_crystal / pdbx_database_status / pdbx_distant_solvent_atoms / pdbx_entity_nonpoly / struct_conn
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _chem_comp.name / _entity.formula_weight / _entity.pdbx_description / _exptl_crystal.density_percent_sol / _pdbx_database_status.process_site / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1Aug 2, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.2Oct 9, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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: PHOSPHOLIPASE A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3974
Polymers13,9891
Non-polymers4083
Water1,54986
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.820, 82.820, 32.800
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein PHOSPHOLIPASE A2


Mass: 13988.814 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gloydius halys (Halys viper) / References: UniProt: P14418, phospholipase A2
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-PBP / p-Bromophenacyl bromide


Mass: 277.941 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H6Br2O
#4: Chemical ChemComp-BU1 / 1,4-BUTANEDIOL


Mass: 90.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / 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: 2.32 Å3/Da / Density % sol: 47.01 %
Crystal growpH: 6.5 / Details: pH 6.5
Crystal grow
*PLUS
Temperature: 18 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
14.5 mg/mlprotein1drop
20.06 M1dropNa(CH3)2AsO2
324.8 %(v/v)1,4-butanediol1drop

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Data collection

DiffractionMean temperature: 290 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Apr 5, 1996
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.93→100 Å / Num. obs: 8600 / % possible obs: 81.06 % / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 12.9 Å2 / Rmerge(I) obs: 0.0619 / Rsym value: 0.0619 / Net I/σ(I): 15.795
Reflection shellResolution: 1.93→2.01 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.034 / Mean I/σ(I) obs: 2.15 / Rsym value: 0.034 / % possible all: 34.6
Reflection shell
*PLUS
% possible obs: 34.6 %

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Processing

Software
NameVersionClassification
XENGENSOFTWAREdata collection
XENGENSOFTWAREdata reduction
X-PLOR3.851model building
X-PLOR3.851refinement
XENGENdata scaling
X-PLOR3.851phasing
RefinementMethod to determine structure: DIFFERENT FOURIER
Starting model: ACIDIC PLA2 (PDB ENTRY 1PSJ)

1psj


Resolution: 2→6 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Details: TOPHBR.PHI,TOPHBR.PRO, TOPHBR.WAT
RfactorNum. reflection% reflectionSelection details
Rfree0.226 801 10.8 %RANDOM
Rwork0.153 ---
obs0.153 7440 87.1 %-
Displacement parametersBiso mean: 24.6 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.17 Å
Luzzati d res low-6 Å
Luzzati sigma a0.07 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 2→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms970 0 17 89 1076
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.013
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_deg2.8
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d22.4
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.14
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.591.5
X-RAY DIFFRACTIONx_mcangle_it2.532
X-RAY DIFFRACTIONx_scbond_it3.012
X-RAY DIFFRACTIONx_scangle_it4.472.5
LS refinement shellResolution: 2→2.09 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.215 78 11.2 %
Rwork0.225 620 -
obs--66 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAMBR.PROTOPHBR.BUT
X-RAY DIFFRACTION2PARAMBR.PBPTOPHBR.ICA
X-RAY DIFFRACTION3TOPHBR.PBP
X-RAY DIFFRACTION4TOPHBR.PEP
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg22.4
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.14
LS refinement shell
*PLUS
Rfactor obs: 0.225

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