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- PDB-1g4i: Crystal structure of the bovine pancreatic phospholipase A2 at 0.97A -

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Basic information

Entry
Database: PDB / ID: 1g4i
TitleCrystal structure of the bovine pancreatic phospholipase A2 at 0.97A
ComponentsPHOSPHOLIPASE A2
KeywordsHYDROLASE / Lipid degradation
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 / phospholipase A2 ...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 / phospholipase A2 / bile acid binding / calcium-dependent phospholipase A2 activity / arachidonate secretion / lipid catabolic process / innate immune response in mucosa / phospholipid binding / antimicrobial humoral immune response mediated by antimicrobial peptide / positive regulation of fibroblast proliferation / fatty acid biosynthetic process / 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 / 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
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 0.97 Å
AuthorsSteiner, R.A. / Rozeboom, H.J. / de Vries, A. / Kalk, K.H. / Murshudov, G.N. / Wilson, K.S. / Dijkstra, B.W.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2001
Title: X-ray structure of bovine pancreatic phospholipase A2 at atomic resolution.
Authors: Steiner, R.A. / Rozeboom, H.J. / de Vries, A. / Kalk, K.H. / Murshudov, G.N. / Wilson, K.S. / Dijkstra, B.W.
History
DepositionOct 27, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Version format compliance
Revision 1.3Aug 9, 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_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 1.4Nov 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4778
Polymers13,8111
Non-polymers6667
Water4,450247
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.532, 63.557, 37.624
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein PHOSPHOLIPASE A2


Mass: 13810.504 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P00593, phospholipase A2

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Non-polymers , 5 types, 254 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


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 247 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.01 Å3/Da / Density % sol: 38.91 %
Crystal growTemperature: 293 K / Method: small tubes / pH: 7.6
Details: MPD, calcium chloride, Tris buffer, pH 7.6, SMALL TUBES, temperature 293K
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
1100 mMTris11
25 mM11CaCl2
330 mg/mlprotein11
4MPD12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.67
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 25, 1999
RadiationMonochromator: 2 crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.67 Å / Relative weight: 1
ReflectionResolution: 0.97→20 Å / Num. all: 66635 / Num. obs: 66635 / % possible obs: 99.8 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 7.04 % / Biso Wilson estimate: 6.373 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 33.4
Reflection shellResolution: 0.97→0.99 Å / Redundancy: 3.28 % / Rmerge(I) obs: 0.172 / Mean I/σ(I) obs: 6.89 / % possible all: 97.4
Reflection
*PLUS
Num. measured all: 469197
Reflection shell
*PLUS
% possible obs: 97.4 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SHELXL-97refinement
RefinementStarting model: PDB ENTRY 1UNE

1une


Resolution: 0.97→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection
Rwork0.094 -
obs0.094 66635
all-66635
Refinement stepCycle: LAST / Resolution: 0.97→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms957 0 42 247 1246
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.021
X-RAY DIFFRACTIONs_angle_d0.046
X-RAY DIFFRACTIONs_from_restr_planes0.0128
X-RAY DIFFRACTIONs_zero_chiral_vol0.111
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.118
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.099
X-RAY DIFFRACTIONs_approx_iso_adps0.076
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Num. reflection all: 63381 / Num. reflection Rfree: 3372 / Rfactor Rfree: 0.1139
Solvent computation
*PLUS
Displacement parameters
*PLUS

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