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- PDB-1zl7: Crystal structure of catalytically-active phospholipase A2 with b... -

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Basic information

Entry
Database: PDB / ID: 1zl7
TitleCrystal structure of catalytically-active phospholipase A2 with bound calcium
Componentshypotensive phospholipase A2
KeywordsHYDROLASE / Asp49-PLA2 / snake venom
Function / homology
Function and homology information


phospholipase A2 activity / phospholipase A2 / arachidonic acid secretion / phospholipid metabolic process / lipid catabolic process / regulation of blood pressure / toxin activity / defense response to bacterium / 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
Acidic phospholipase A2 BthA-1
Similarity search - Component
Biological speciesBothrops jararacussu (jararacussu)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsMurakami, M.T. / Cintra, A.C. / Gabdoulkhakov, A. / Genov, N. / Betzel, C. / Arni, R.K.
Citation
Journal: Biochimie / Year: 2006
Title: Insights into metal ion binding in phospholipases A(2): ultra high-resolution crystal structures of an acidic phospholipase A(2) in the Ca(2+) free and bound states.
Authors: Murakami, M.T. / Gabdoulkhakov, A. / Genov, N. / Cintra, A.C. / Betzel, C. / Arni, R.K.
#1: Journal: Biochim.Biophys.Acta / Year: 2004
Title: Crystallization and high-resolution X-ray diffraction data collection of an Asp49 PLA2 from Bothrops jararacussu venom both in the presence and absence of Ca2+ ions.
Authors: Murakami, M.T. / Michelan-Duarte, S. / Cintra, A.C.O. / Arni, R.K.
History
DepositionMay 5, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 25, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Aug 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 / 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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: hypotensive phospholipase A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8313
Polymers13,6981
Non-polymers1322
Water1,892105
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: hypotensive phospholipase A2
hetero molecules

A: hypotensive phospholipase A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6616
Polymers27,3972
Non-polymers2644
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area2680 Å2
ΔGint-21 kcal/mol
Surface area11180 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)39.206, 53.218, 90.057
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein hypotensive phospholipase A2


Mass: 13698.481 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: venom / Source: (natural) Bothrops jararacussu (jararacussu) / References: UniProt: Q8AXY1, 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 105 / Source method: isolated from a natural source / Formula: H2O

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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: 1.72 Å3/Da / Density % sol: 27.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG 3350, CaCl2, tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.427 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 20, 2004
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.427 Å / Relative weight: 1
ReflectionResolution: 1.6→30 Å / Num. obs: 12748 / % possible obs: 99.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.047
Reflection shellResolution: 1.6→1.63 Å / Rmerge(I) obs: 0.482 / % possible all: 98.9

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MAR345data collection
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1UMV

1umv


Resolution: 1.6→22.9 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.944 / SU B: 1.992 / SU ML: 0.071 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / ESU R: 0.193 / ESU R Free: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23199 606 4.8 %RANDOM
Rwork0.1763 ---
all0.205 ---
obs0.17892 12723 99.1 %-
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: 24.034 Å2
Baniso -1Baniso -2Baniso -3
1-0.25 Å20 Å20 Å2
2---0.24 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.6→22.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms950 0 7 105 1062
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0211004
X-RAY DIFFRACTIONr_angle_refined_deg1.7221.9621357
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0265125
X-RAY DIFFRACTIONr_chiral_restr0.130.2133
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02773
X-RAY DIFFRACTIONr_nbd_refined0.2420.2586
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.180.2105
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1850.263
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2730.225
X-RAY DIFFRACTIONr_mcbond_it1.3071.5616
X-RAY DIFFRACTIONr_mcangle_it2.1062984
X-RAY DIFFRACTIONr_scbond_it2.813388
X-RAY DIFFRACTIONr_scangle_it4.0224.5373
X-RAY DIFFRACTIONr_rigid_bond_restr1.46521004
X-RAY DIFFRACTIONr_sphericity_free3.582106
X-RAY DIFFRACTIONr_sphericity_bonded3.0372974
LS refinement shellResolution: 1.6→1.64 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.313 50
Rwork0.208 875

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