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- PDB-2b96: Third Calcium ion found in an inhibitor bound phospholipase A2 -

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Basic information

Entry
Database: PDB / ID: 2b96
TitleThird Calcium ion found in an inhibitor bound phospholipase A2
ComponentsPhospholipase A2
KeywordsHYDROLASE / Alpha Helix / Beta Sheet / triple mutant / anisic acid
Function / homology
Function and homology information


Acyl chain remodelling of PS / Acyl chain remodelling of PG / Synthesis of PA / Acyl chain remodelling of PC / Acyl chain remodelling of PE / Acyl chain remodelling of PI / positive regulation of podocyte apoptotic process / phosphatidylglycerol metabolic process / phosphatidylcholine metabolic process / calcium-dependent phospholipase A2 activity ...Acyl chain remodelling of PS / Acyl chain remodelling of PG / Synthesis of PA / Acyl chain remodelling of PC / Acyl chain remodelling of PE / Acyl chain remodelling of PI / positive regulation of podocyte apoptotic process / phosphatidylglycerol metabolic process / phosphatidylcholine metabolic process / calcium-dependent phospholipase A2 activity / phospholipase A2 / bile acid binding / arachidonic acid secretion / phospholipid metabolic process / lipid catabolic process / innate immune response in mucosa / phospholipid binding / fatty acid biosynthetic process / positive regulation of fibroblast proliferation / antimicrobial humoral immune response mediated by antimicrobial peptide / antibacterial humoral response / defense response to Gram-positive bacterium / signaling receptor binding / calcium ion binding / cell surface / extracellular space
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
4-METHOXYBENZOIC ACID / Phospholipase A2
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / Molecular Placement / Resolution: 1.7 Å
AuthorsSekar, K. / Velmurugan, D. / Yamane, T. / Tsai, M.D.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2006
Title: Third Calcium ion found in an inhibitor bound phospholipase A2
Authors: Sekar, K. / Gayathri, D. / Velmurugan, D. / Jeyakanthan, J. / Yamane, T. / Poi, M.J. / Tsai, M.D.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2005
Title: Atomic resolution (0.97 A) structure of the triple mutant (K53,56,121M) of bovine pancreatic phospholipase A2
Authors: Sekar, K. / Rajakannan, V. / Gayathri, D. / Velmurugan, D. / Poi, M.J. / Dauter, M. / Dauter, Z. / Tsai, M.D.
#2: Journal: J.Mol.Biol. / Year: 2003
Title: Crystal structures of the free and anisic acid bound triple mutant of phospholipase A2.
Authors: Sekar, K. / Mala, S.V. / Yogavel, M. / Velmurugan, D. / Poi, M.J. / Vishwanath, B.S. / Gowda, T.V. / Jeyaprakash, A.A. / Tsai, M.D.
#3: Journal: J.Mol.Biol. / Year: 2002
Title: Observation of additional calcium ion in the crystal structure of the triple mutant K56,120,121M of bovine pancreatic phospholipase A2.
Authors: Rajakannan, V. / Yogavel, M. / Poi, M.J. / Jeyaprakash, A.A. / Jeyakanthan, J. / Velmurugan, D. / Tsai, M.D. / Sekar, K.
#4: Journal: Acta Crystallogr.,Sect.D / Year: 1999
Title: High-resolution refinement of orthorhombic bovine pancreatic phospholipase A2.
Authors: Sekar, K. / Sundaralingam, M.
#5: Journal: Biochemistry / Year: 1997
Title: Phospholipase A2 engineering. Structural and functional roles of the highly conserved active site residue aspartate-99.
Authors: Sekar, K. / Yu, B.Z. / Rogers, J. / Lutton, J. / Liu, X. / Chen, X. / Tsai, M.D. / Jain, M.K. / Sundaralingam, M.
History
DepositionOct 11, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 28, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / 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_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.ptnr1_symmetry / _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.ptnr3_symmetry / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phospholipase A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,61310
Polymers13,8171
Non-polymers7969
Water2,252125
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.190, 46.190, 102.860
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Phospholipase A2 / / Phosphatidylcholine 2- acylhydrolase / Group IB phospholipase A2


Mass: 13816.552 Da / Num. of mol.: 1 / Mutation: K53M, K56M, K121M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: PLA2G1B / Production host: Escherichia coli (E. coli) / Strain (production host): BOS Taurus / References: UniProt: P00593, phospholipase A2

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Non-polymers , 5 types, 134 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Chemical ChemComp-ANN / 4-METHOXYBENZOIC ACID / P-ANISIC ACID / P-Anisic acid


Mass: 152.147 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 125 / 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: 2.29 Å3/Da / Density % sol: 46.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 50 mM Tris Buffer, 70% MPD reservoir, 15-20 mg/ml protein, 5mM CaCl2, 1microlitre anisic acid, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE
DetectorDetector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.7→20 Å / Num. obs: 14435 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.132
Reflection shellResolution: 1.7→1.81 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.132 / Num. unique all: 116129 / % possible all: 94.7

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALAdata scaling
CNSrefinement
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: Molecular Placement
Starting model: 1MKT

1mkt


Resolution: 1.7→20 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: As implemented in CNS
RfactorNum. reflection% reflectionSelection details
Rfree0.221 727 -random
Rwork0.202 ---
all-14469 --
obs-14435 98.9 %-
Displacement parametersBiso mean: 23.6 Å2
Baniso -1Baniso -2Baniso -3
1-1.35 Å21.66 Å20 Å2
2--1.35 Å20 Å2
3----2.71 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 1.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms954 0 47 125 1126
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_d2
X-RAY DIFFRACTIONc_dihedral_angle_d22.5
X-RAY DIFFRACTIONc_improper_angle_d1.62
LS refinement shellResolution: 1.7→1.76 Å / Rfactor Rfree error: 0.008
RfactorNum. reflection% reflection
Rfree0.221 727 -
Rwork0.202 --
obs-14435 98.9 %

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