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- PDB-1ijl: Crystal structure of acidic phospholipase A2 from deinagkistrodon... -

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Basic information

Entry
Database: PDB / ID: 1ijl
TitleCrystal structure of acidic phospholipase A2 from deinagkistrodon acutus
ComponentsPHOSPHOLIPASE A2
KeywordsHYDROLASE / THREE LONG HELIX / ONE TWO STRAND BETA SHEET / CALCIUM BINDING LOOP
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
Acidic phospholipase A2
Similarity search - Component
Biological speciesDeinagkistrodon acutus (Chinese moccasin)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsGu, L. / Zhang, H. / Song, S. / Zhou, Y. / Lin, Z.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2002
Title: Structure of an acidic phospholipase A2 from the venom of Deinagkistrodon acutus.
Authors: Gu, L. / Zhang, H. / Song, S. / Zhou, Y. / Lin, Z.
#1: Journal: ACTA BIOCHIM.BIOPHYS.SINICA / Year: 1999
Title: Cloning and sequencing of gene encoding Phospholipase A2 from Agkistrodon Acutus
Authors: Liu, X.L. / Pan, H. / Yang, G.Z. / Wu, X.F. / Zhou, Y.C.
History
DepositionApr 27, 2001Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 28, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_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_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 1.4Oct 16, 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)28,3295
Polymers28,1832
Non-polymers1463
Water1,69394
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2160 Å2
ΔGint-40 kcal/mol
Surface area12490 Å2
MethodPISA
2
A: PHOSPHOLIPASE A2
hetero molecules

B: PHOSPHOLIPASE A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3295
Polymers28,1832
Non-polymers1463
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_647-x+1,y-1/2,-z+21
Buried area430 Å2
ΔGint-63 kcal/mol
Surface area14320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.710, 38.000, 69.900
Angle α, β, γ (deg.)90.00, 99.35, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein PHOSPHOLIPASE A2


Mass: 14091.680 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Deinagkistrodon acutus (Chinese moccasin) / References: UniProt: Q7SID6, phospholipase A2
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 94 / 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: 2.26 Å3/Da / Density % sol: 45.67 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: MPD, sodium chloride, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291.0K
Crystal grow
*PLUS
Temperature: 291 K
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mg/mlprotein1drop
20.05 MHEPES1droppH7.5
30.07 M1dropNaCl
412 %MPD1drop
50.1 MHEPES1reservoirpH7.5
670 %MPD1reservoir

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Data collection

DiffractionMean temperature: 291 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 1, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. all: 8966 / Num. obs: 8966 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9 % / Biso Wilson estimate: 30.5 Å2 / Rmerge(I) obs: 0.122 / Net I/σ(I): 14.1
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.403 / Mean I/σ(I) obs: 3.3 / Num. unique all: 898 / % possible all: 100
Reflection
*PLUS
Num. measured all: 80310
Reflection shell
*PLUS
% possible obs: 100 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PSJ

1psj


Resolution: 2.6→8 Å / Isotropic thermal model: isotropic / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.225 816 -RANDOM
Rwork0.184 ---
all-7706 --
obs-7703 99.96 %-
Displacement parametersBiso mean: 36.6 Å2
Baniso -1Baniso -2Baniso -3
1--1.7 Å20 Å2-
2--1.7 Å20 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.29 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 2.6→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1923 0 3 94 2020
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.07
X-RAY DIFFRACTIONc_angle_deg1.247
X-RAY DIFFRACTIONc_dihedral_angle_d23.924
X-RAY DIFFRACTIONc_improper_angle_d0.80594
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-IDNum. reflection obs% reflection obs (%)
2.6-2.690.317710.23X-RAY DIFFRACTION780100
2.69-2.790.257770.234X-RAY DIFFRACTION750100
2.79-2.910.259910.217X-RAY DIFFRACTION78299.9
2.91-3.060.211890.194X-RAY DIFFRACTION756100
3.06-3.240.225800.188X-RAY DIFFRACTION756100
3.24-3.470.229720.181X-RAY DIFFRACTION77399.7
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 8 Å / σ(F): 0 / Rfactor obs: 0.184 / Rfactor Rfree: 0.225
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 36.6 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.07
X-RAY DIFFRACTIONc_angle_deg1.22
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.88
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.79
LS refinement shell
*PLUS
Highest resolution: 2.6 Å / Rfactor Rfree: 0.317 / Rfactor Rwork: 0.23

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