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- PDB-1ln8: Crystal Structure of a New Isoform of Phospholipase A2 from Naja ... -

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Basic information

Entry
Database: PDB / ID: 1ln8
TitleCrystal Structure of a New Isoform of Phospholipase A2 from Naja naja sagittifera at 1.6 A Resolution
ComponentsPhospholipase A2
KeywordsHYDROLASE / phospholipase A2 / isoform / naja naja sagittifera
Function / homology
Function and homology information


phospholipase A2 / phospholipase A2 activity / arachidonic acid secretion / phospholipid metabolic process / lipid catabolic process / calcium ion binding / extracellular region
Similarity search - Function
Phospholipase A2, aspartic acid active site / Phospholipase A2 aspartic acid active site. / Phospholipase A2, histidine active site / Phospholipase A2 histidine active site. / Phospholipase A2 / Phospholipase A2 domain / Phospholipase A2 / Phospholipase A2 / Phospholipase A2 / Phospholipase A2 domain ...Phospholipase A2, aspartic acid active site / Phospholipase A2 aspartic acid active site. / Phospholipase A2, histidine active site / Phospholipase A2 histidine active site. / Phospholipase A2 / Phospholipase A2 domain / Phospholipase A2 / Phospholipase A2 / Phospholipase A2 / Phospholipase A2 domain / Phospholipase A2 domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
PHOSPHATE ION / Acidic phospholipase A2 3
Similarity search - Component
Biological speciesNaja sagittifera (cobra)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsSingh, R.K. / Vikram, P. / Paramasivam, M. / Jabeen, T. / Sharma, S. / Kaur, P. / Srinivasan, A. / Singh, T.P.
Citation
Journal: to be published
Title: Crystal Structure of a New Form of Phospholipase A2 from Naja naja sagittifera at 1.6 A Resolution
Authors: Singh, R.K. / Vikram, P. / Paramasivam, M. / Jabeen, T. / Sharma, S. / Kaur, P. / Srinivasan, A. / Singh, T.P.
#1: Journal: to be published
Title: Crystal Structure Of An Acidic Phospholipase A2 From Naja Naja Sagittifera At 1.5 A Resolution
Authors: Singh, R.K. / Sharma, S. / Jabeen, T. / Kaur, P. / Singh, T.P.
History
DepositionMay 3, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 20, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 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 / diffrn_source / 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 / _diffrn_source.pdbx_synchrotron_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_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

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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)13,2643
Polymers13,1291
Non-polymers1352
Water2,666148
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.099, 42.099, 64.549
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein Phospholipase A2 /


Mass: 13128.515 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Naja sagittifera (cobra) / Secretion: venom / References: UniProt: P60045, 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-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 148 / 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: 2.18 Å3/Da / Density % sol: 43.23 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: sodium phosphate, ethanol, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.802 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 14, 2001 / Details: Mirror
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.802 Å / Relative weight: 1
ReflectionResolution: 1.65→20 Å / Num. all: 13470 / Num. obs: 12931 / % possible obs: 99 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 7.1 % / Biso Wilson estimate: 20.429 Å2 / Rsym value: 0.078 / Net I/σ(I): 18.2
Reflection shellResolution: 1.65→1.68 Å / Mean I/σ(I) obs: 3 / Num. unique all: 672 / Rsym value: 0.299 / % possible all: 99.1

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMAC5refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LFF

1lff
PDB Unreleased entry


Resolution: 1.65→20 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.94 / SU B: 2.871 / SU ML: 0.099 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.108 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22193 539 4 %RANDOM
Rwork0.18408 ---
all0.1855 13470 --
obs0.18558 12931 100 %-
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: 20.147 Å2
Baniso -1Baniso -2Baniso -3
1--0.25 Å20 Å20 Å2
2---0.25 Å20 Å2
3---0.5 Å2
Refine analyzeLuzzati coordinate error obs: 0.19 Å / Luzzati sigma a obs: 0.12 Å
Refinement stepCycle: LAST / Resolution: 1.65→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms910 0 6 148 1064
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.021939
X-RAY DIFFRACTIONr_bond_other_d0.0010.02739
X-RAY DIFFRACTIONr_angle_refined_deg1.4911.9451276
X-RAY DIFFRACTIONr_angle_other_deg0.97331735
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.3933117
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.86915141
X-RAY DIFFRACTIONr_chiral_restr0.0880.2129
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021084
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02196
X-RAY DIFFRACTIONr_nbd_refined0.2670.3246
X-RAY DIFFRACTIONr_nbd_other0.1990.3727
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1360.5106
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2340.316
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2420.342
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2180.518
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.7441.5589
X-RAY DIFFRACTIONr_mcangle_it1.4722934
X-RAY DIFFRACTIONr_scbond_it2.333350
X-RAY DIFFRACTIONr_scangle_it3.5484.5342
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.277 46
Rwork0.217 937

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