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- PDB-2bax: Atomic Resolution Structure of the Double Mutant (K53,56M) of Bov... -

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Entry
Database: PDB / ID: 2bax
TitleAtomic Resolution Structure of the Double Mutant (K53,56M) of Bovine Pancreatic Phospholipase A2
ComponentsPhospholipase A2
KeywordsHYDROLASE / Phospholipase A2 / alpha helix / beta sheet
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 / calcium-dependent phospholipase A2 activity / phosphatidylcholine metabolic process ...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 / calcium-dependent phospholipase A2 activity / phosphatidylcholine metabolic process / 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
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å
AuthorsSekar, K. / Yogavel, M. / Velmurugan, D. / Dauter, Z. / Dauter, M. / Tsai, M.D.
Citation
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.
#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 15, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 25, 2005Provider: 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 / 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 / _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)14,4818
Polymers13,8151
Non-polymers6667
Water3,765209
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.057, 46.057, 101.138
Angle α, β, γ (deg.)90, 90, 120
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-213-

HOH

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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: 13814.536 Da / Num. of mol.: 1 / Mutation: K53M, K56M
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): pTO-A2MBL21 / References: UniProt: P00593, phospholipase A2

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Non-polymers , 5 types, 216 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / 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-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 209 / 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: 2.24 Å3/Da / Density % sol: 45.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.2
Details: The double mutant protein was dissolved in 50 mM Tris buffer (7.2) containing 5mM of CaCl2, to a final protein Concentration of 17-20 mg/ml. The crystallization droplet contained 5 micro ...Details: The double mutant protein was dissolved in 50 mM Tris buffer (7.2) containing 5mM of CaCl2, to a final protein Concentration of 17-20 mg/ml. The crystallization droplet contained 5 micro litre of protein and 2 micro litre of 60% MPD and the reservior contianined 1000 micro litre of 70% MPD, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 15, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.1→20 Å / Num. obs: 50297 / % possible obs: 98.2 % / Observed criterion σ(F): 4 / Rmerge(I) obs: 0.044
Reflection shellResolution: 1.1→1.14 Å / Rmerge(I) obs: 0.216 / Num. unique all: 50297 / % possible all: 99

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALAdata scaling
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1C74

1c74


Resolution: 1.1→20 Å / Cross valid method: THROUGHOUT / σ(F): 4 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.156 -Random
Rwork0.119 --
all0.119 --
obs0.114 50297 -
Refinement stepCycle: LAST / Resolution: 1.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1251 0 2 348 1601
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_angle_d0.028
LS refinement shellResolution: 1.1→1.14 Å
RfactorNum. reflection% reflection
Rfree0.156 2510 -
Rwork0.119 --
obs-50297 98.2 %

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