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- PDB-1rlw: CALCIUM-PHOSPHOLIPID BINDING DOMAIN FROM CYTOSOLIC PHOSPHOLIPASE A2 -

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Basic information

Entry
Database: PDB / ID: 1rlw
TitleCALCIUM-PHOSPHOLIPID BINDING DOMAIN FROM CYTOSOLIC PHOSPHOLIPASE A2
ComponentsPHOSPHOLIPASE A2
KeywordsHYDROLASE / C2 DOMAIN / CALB DOMAIN
Function / homology
Function and homology information


platelet activating factor biosynthetic process / phosphatidylglycerol catabolic process / Arachidonic acid metabolism / icosanoid metabolic process / Acyl chain remodeling of CL / monoacylglycerol biosynthetic process / glycerophospholipid catabolic process / Hydrolysis of LPC / phosphatidyl phospholipase B activity / lysophospholipase ...platelet activating factor biosynthetic process / phosphatidylglycerol catabolic process / Arachidonic acid metabolism / icosanoid metabolic process / Acyl chain remodeling of CL / monoacylglycerol biosynthetic process / glycerophospholipid catabolic process / Hydrolysis of LPC / phosphatidyl phospholipase B activity / lysophospholipase / O-acyltransferase activity / phosphatidylcholine acyl-chain remodeling / Acyl chain remodelling of PG / calcium-independent phospholipase A2 activity / Acyl chain remodelling of PC / Acyl chain remodelling of PI / Acyl chain remodelling of PS / Acyl chain remodelling of PE / ceramide 1-phosphate binding / Synthesis of PA / arachidonic acid metabolic process / glycerol metabolic process / positive regulation of T-helper 1 type immune response / phosphatidylcholine catabolic process / phosphatidylinositol-5-phosphate binding / positive regulation of prostaglandin secretion / lysophospholipase activity / phospho-PLA2 pathway / phospholipase A2 activity / COPI-independent Golgi-to-ER retrograde traffic / phosphatidylinositol-3-phosphate binding / leukotriene biosynthetic process / calcium-dependent phospholipid binding / calcium-dependent phospholipase A2 activity / positive regulation of macrophage activation / positive regulation of platelet activation / phosphatidylinositol-4-phosphate binding / phospholipase A2 / prostaglandin biosynthetic process / cellular response to antibiotic / arachidonic acid secretion / Platelet sensitization by LDL / establishment of localization in cell / ADP signalling through P2Y purinoceptor 1 / nuclear envelope / regulation of cell population proliferation / mitochondrial inner membrane / Golgi membrane / intracellular membrane-bounded organelle / calcium ion binding / endoplasmic reticulum membrane / Golgi apparatus / endoplasmic reticulum / nucleus / cytosol / cytoplasm
Similarity search - Function
Lysophospholipase, catalytic domain / Cytosolic phospholipase A2, C2 domain / Lysophospholipase catalytic domain / PLA2c domain profile. / Cytoplasmic phospholipase A2, catalytic subunit / C2 domain / Acyl transferase/acyl hydrolase/lysophospholipase / C2 domain / Protein kinase C conserved region 2 (CalB) / C2 domain ...Lysophospholipase, catalytic domain / Cytosolic phospholipase A2, C2 domain / Lysophospholipase catalytic domain / PLA2c domain profile. / Cytoplasmic phospholipase A2, catalytic subunit / C2 domain / Acyl transferase/acyl hydrolase/lysophospholipase / C2 domain / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain profile. / C2 domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / Cytosolic phospholipase A2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.4 Å
AuthorsPerisic, O. / Williams, R.L.
CitationJournal: J.Biol.Chem. / Year: 1998
Title: Crystal structure of a calcium-phospholipid binding domain from cytosolic phospholipase A2.
Authors: Perisic, O. / Fong, S. / Lynch, D.E. / Bycroft, M. / Williams, R.L.
History
DepositionOct 28, 1997Processing site: BNL
Revision 1.0Feb 25, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / diffrn_source ...database_2 / diffrn_source / 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 / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.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 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)14,6045
Polymers14,2991
Non-polymers3054
Water2,720151
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.410, 79.410, 70.670
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein PHOSPHOLIPASE A2 / / CALB DOMAIN


Mass: 14299.154 Da / Num. of mol.: 1 / Fragment: C2 DOMAIN, RESIDUES 17 - 141 FROM CPLA2 / Mutation: Y16S, C139A, C141S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cellular location: CYTOSOL / Plasmid: MINI-PRSETA / Production host: Escherichia coli (E. coli) / Strain (production host): BLR / Variant (production host): DE3 / References: UniProt: P47712, phospholipase A2
#2: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cd
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 151 / 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: 5 Å3/Da / Density % sol: 70 %
Crystal growpH: 7.5
Details: 5-10MG/ML PROTEIN, 5MM CACL2, 1M SODIUM ACETATE, 0.1M HEPES (PH 7.5), 50MM CDSO4
Crystal grow
*PLUS
Temperature: 21 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
12.5-5 mg/mlprotein1drop
22.5 mM1dropCaCl2
30.5 Msodium acetate1drop
40.05 MHEPES1drop
525 mM1dropCdSO4
61 Msodium acetate1reservoir
70.1 MHEPES1reservoir
850 mM1reservoirCdSO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8838
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 7, 1997 / Details: BENT MIRROR
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8838 Å / Relative weight: 1
ReflectionResolution: 2.3→31 Å / Num. obs: 11798 / % possible obs: 98.8 % / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Biso Wilson estimate: 41 Å2 / Rmerge(I) obs: 0.086 / Rsym value: 0.086 / Net I/σ(I): 18
Reflection shellResolution: 2.3→2.35 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 3.4 / Rsym value: 0.31 / % possible all: 86
Reflection
*PLUS
Num. measured all: 52266

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Processing

Software
NameVersionClassification
SHARPphasing
REFMACrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MIR / Resolution: 2.4→15 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.273 1003 10 %SHELLS OF RESOLUTION
Rwork0.227 ---
obs-9339 99.7 %-
Displacement parametersBiso mean: 25 Å2
Refine analyzeLuzzati d res low obs: 8 Å / Luzzati sigma a obs: 0.03 Å
Refinement stepCycle: LAST / Resolution: 2.4→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 0 151 1152
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0070.02
X-RAY DIFFRACTIONp_angle_d0.0250.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0250.05
X-RAY DIFFRACTIONp_hb_or_metal_coord0.2510.08
X-RAY DIFFRACTIONp_mcbond_it1.0122
X-RAY DIFFRACTIONp_mcangle_it1.7642.5
X-RAY DIFFRACTIONp_scbond_it31.04
X-RAY DIFFRACTIONp_scangle_it2.0613
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr0.0970.15
X-RAY DIFFRACTIONp_singtor_nbd0.1910.3
X-RAY DIFFRACTIONp_multtor_nbd0.2320.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor4.17
X-RAY DIFFRACTIONp_staggered_tor20.115
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor26.320
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Num. reflection all: 10342 / Rfactor obs: 0.228
Solvent computation
*PLUS
Displacement parameters
*PLUS

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