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- PDB-1jia: STRUCTURE OF A BASIC PHOSPHOLIPASE A2 FROM AGKISTRODON HALYS PALL... -

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Basic information

Entry
Database: PDB / ID: 1jia
TitleSTRUCTURE OF A BASIC PHOSPHOLIPASE A2 FROM AGKISTRODON HALYS PALLAS AT 2.13A RESOLUTION
ComponentsPHOSPHOLIPASE A2
KeywordsPHOSPHOLIPASE / PHOSPHOLIPASE A2 / AGKISTRODON HALYS PALLAS CRYSTAL STRUCTURE
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 / STRUCTURE REFINEMENT / Resolution: 2.13 Å
AuthorsZhao, K. / Lin, Z.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1998
Title: Structure of a basic phospholipase A2 from Agkistrodon halys Pallas at 2.13 A resolution.
Authors: Zhao, K. / Song, S. / Lin, Z. / Zhou, Y.
#1: Journal: Shengwu Huaxue Zazhi / Year: 1997
Title: Preliminary Crystallographic Studies of a Basic Phospholipase A2 from the Venom of Agkistrodon Halys Pallas
Authors: Zhao, K. / Song, S. / Lin, Z. / Zhou, Y.
History
DepositionJun 9, 1997Processing site: BNL
Revision 1.0Jun 10, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PHOSPHOLIPASE A2
B: PHOSPHOLIPASE A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9264
Polymers27,8462
Non-polymers802
Water3,423190
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)97.130, 103.690, 23.270
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.10143, -0.99475, -0.01393), (0.99469, 0.10165, -0.01605), (0.01739, -0.01223, 0.99977)
Vector: 21.71425, -26.07776, -5.96769)

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Components

#1: Protein PHOSPHOLIPASE A2


Mass: 13923.168 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Gloydius halys (Halys viper) / Cellular location: EXTRACELLULAR / Secretion: VENOM / References: UniProt: O42187, phospholipase A2
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 190 / 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: 2.09 Å3/Da / Density % sol: 37 %
Description: THE STRUCTURE OF BASIC PLA2 FROM AGKISTRODON HALYS PALLAS WAS DETERMINED BY MOLECULAR REPLACEMENT METHOD, USING R CHAIN OF PLA2 FROM THE VENOM OF WESTERN DIAMONDBACK RATTLESNAKE(2.5A) AS A SEARCH MODEL.
Crystal growpH: 9.5
Details: THE PROTEIN SOLUTIONS CONTAINED 10MM CA2+, 0.1M NACL, 5% PEG 4K IN 0.01M CHESS BUFFER (PH 9.5) AND AN ENZYME CONCENTRATION OF 11MG/ML; THE SOLUTION IN RESERVOIR CONTAINED 10% PEG 4K IN SAME ...Details: THE PROTEIN SOLUTIONS CONTAINED 10MM CA2+, 0.1M NACL, 5% PEG 4K IN 0.01M CHESS BUFFER (PH 9.5) AND AN ENZYME CONCENTRATION OF 11MG/ML; THE SOLUTION IN RESERVOIR CONTAINED 10% PEG 4K IN SAME BUFFER, ROOM TEMPERATURE OF 17 DEGREES C.
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
112 mg/mlprotein1drop
20.05 MCHES1drop
30.1 M1dropNaCl
45 %(w/v)PEG40001drop
510 mg/ml1dropCaCl2
60.05 MCHES1reservoir
70.2 M1reservoirNaCl
810 %(w/v)PEG40001reservoir
920 mg/ml1reservoirCaCl2

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Data collection

DiffractionMean temperature: 280 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: SIEMENS-NICOLET X200B / Detector: AREA DETECTOR / Date: May 1, 1995
RadiationMonochromator: NICKEL / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.13→40 Å / Num. obs: 12001 / % possible obs: 86.1 % / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Biso Wilson estimate: 26.24 Å2 / Rmerge(I) obs: 0.0459 / Net I/σ(I): 31.2
Reflection shellResolution: 2.13→2.23 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.176 / Mean I/σ(I) obs: 4.9 / % possible all: 46.28
Reflection
*PLUS
Num. measured all: 29753
Reflection shell
*PLUS
% possible obs: 46.28 %

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Processing

Software
NameClassification
XENGENdata collection
XENGENdata reduction
X-PLORmodel building
X-PLORrefinement
XENGENdata scaling
X-PLORphasing
RefinementMethod to determine structure: STRUCTURE REFINEMENT / Resolution: 2.13→6 Å
Cross valid method: FULL REFINEMENT CONSISTING OF INITIAL MINIMIZATION, SLOW COOLING-SA 3000K, POSITIONAL AND B-FACTOR REFINEMENT.
σ(F): 3
Details: DURING THE REFINEMENT, NO NCS RESTRAINTS WERE USED.
RfactorNum. reflection% reflectionSelection details
Rfree0.255 1063 10.45 %RANDOM
Rwork0.152 ---
obs0.152 10174 77.8 %-
Displacement parametersBiso mean: 25.41 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å / Luzzati d res low obs: 6 Å
Refinement stepCycle: LAST / Resolution: 2.13→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1916 0 2 190 2108
Refine LS restraints
Refine-IDTypeDev ideal
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_deg2.72
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.4
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.29
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
LS refinement shellResolution: 2.13→2.22 Å / Total num. of bins used: 1
RfactorNum. reflection% reflection
Rfree0.335 50 9.8 %
Rwork0.242 459 -
obs--46.28 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19X.PROTOPH19X.PRO
X-RAY DIFFRACTION2PARAM.WATTOPOLOGY.WAT
Software
*PLUS
Name: X-PLOR / 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_deg23.4
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.29
LS refinement shell
*PLUS
Rfactor obs: 0.242

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