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- PDB-1s8g: Crystal structure of Lys49-Phospholipase A2 from Agkistrodon cont... -

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Basic information

Entry
Database: PDB / ID: 1s8g
TitleCrystal structure of Lys49-Phospholipase A2 from Agkistrodon contortrix laticinctus, fatty acid bound form
ComponentsPhospholipase A2 homolog
Keywordshydrolase / toxin / Lys49-Phospholipase A2 / snake venom / myotoxicity / fatty acid bound form
Function / homology
Function and homology information


calcium-dependent phospholipase A2 activity / arachidonate secretion / lipid catabolic process / phospholipid metabolic process / negative regulation of T cell proliferation / phospholipid binding / heparin 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
LAURIC ACID / Basic phospholipase A2 homolog MT1
Similarity search - Component
Biological speciesAgkistrodon contortrix laticinctus (broad-banded copperhead)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsAmbrosio, A.L.B. / de Souza, D.H.F. / Nonato, M.C. / Selistre de Araujo, H.S. / Ownby, C.L. / Garratt, R.C.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: A Molecular Mechanism for Lys49-Phospholipase A2 Activity Based on Ligand-induced Conformational Change.
Authors: Ambrosio, A.L.B. / Nonato, M.C. / Selistre de Araujo, H.S. / Arni, R. / Ward, R.J. / Ownby, C.L. / de Souza, D.H.F. / Garratt, R.C.
History
DepositionFeb 2, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 10, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Aug 23, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 13, 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: Phospholipase A2 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4384
Polymers14,0491
Non-polymers3883
Water1,40578
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.897, 81.897, 49.902
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Phospholipase A2 homolog / Myotoxin


Mass: 14049.392 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Snake venom protein
Source: (natural) Agkistrodon contortrix laticinctus (broad-banded copperhead)
Species: Agkistrodon contortrix / Strain: laticinctus / References: UniProt: P49121, phospholipase A2
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-DAO / LAURIC ACID


Mass: 200.318 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H24O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / 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: 3 Å3/Da / Density % sol: 58.64 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: cacodylate, ammonium sulfate, PEG 8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
Temperature: 291 K / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
130 %(w/v)PEG80001reservoir
20.1 Msodium cacodylate1reservoirpH6.5
30.2 Mammonium sulfate1reservoir
410 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.544 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Oct 11, 2001 / Details: mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.544 Å / Relative weight: 1
ReflectionResolution: 2.3→57.3 Å / Num. all: 7960 / Num. obs: 7960 / % possible obs: 98.1 % / Observed criterion σ(I): 1.7 / Redundancy: 6.2 % / Rmerge(I) obs: 0.118 / Rsym value: 0.118
Reflection shellResolution: 2.3→2.41 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.118 / Mean I/σ(I) obs: 1.7 / Rsym value: 0.118 / % possible all: 99.7
Reflection
*PLUS
Num. measured all: 101833
Reflection shell
*PLUS
Lowest resolution: 2.36 Å / % possible obs: 99.7 % / Rmerge(I) obs: 0.382

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PPA

1ppa


Resolution: 2.3→57.3 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.92 / SU B: 6.687 / SU ML: 0.157 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.282 / ESU R Free: 0.222 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24721 356 4.6 %RANDOM
Rwork0.20457 ---
obs0.20663 7387 97.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 41.135 Å2
Baniso -1Baniso -2Baniso -3
1--1.72 Å20 Å20 Å2
2---1.72 Å20 Å2
3---3.45 Å2
Refinement stepCycle: LAST / Resolution: 2.3→57.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms972 0 25 78 1075
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0211005
X-RAY DIFFRACTIONr_bond_other_d0.0020.02859
X-RAY DIFFRACTIONr_angle_refined_deg0.9291.9771348
X-RAY DIFFRACTIONr_angle_other_deg0.72632026
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6735120
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0510.2136
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.021082
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02196
X-RAY DIFFRACTIONr_nbd_refined0.1690.2215
X-RAY DIFFRACTIONr_nbd_other0.1940.21003
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0820.2556
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1310.267
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1460.22
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2250.217
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1310.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.2471.5600
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.4912961
X-RAY DIFFRACTIONr_scbond_it0.6723405
X-RAY DIFFRACTIONr_scangle_it1.1694.5387
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.407 19
Rwork0.276 549
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.2578-0.12580.29311.33120.39571.70.0185-0.14980.1209-0.04150.12650.00190.09070.2051-0.1450.06030.03320.03340.0659-0.02470.070419.422936.2884.057
262.286-252.4038114.3531-89.463186.6442160.3429-0.21722.42933.3603-5.38711.80110.4523-0.2113-0.5836-1.5840.11260.0316-0.00460.1314-0.01610.113117.818124.850110.3195
3-10.8733-28.05695.758174.9259-147.204352.4348-1.16372.0714-0.1027-1.7352-4.7061-2.91273.42271.83915.86970.13110.0162-0.00040.1203-0.02680.122823.161735.0175-1.809
469.918335.1226380.9407551.8273-216.8514245.0231-0.08680.7810.20911.7353-0.18312.90980.28152.35460.26990.1206-0.00110.01160.12460.00770.130620.969930.35021.9366
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 1331 - 121
2X-RAY DIFFRACTION2AB134
3X-RAY DIFFRACTION3AC135
4X-RAY DIFFRACTION4AD136
Refinement
*PLUS
Highest resolution: 2.3 Å / Rfactor Rfree: 0.247 / Rfactor Rwork: 0.205
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.005
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg0.929

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