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- PDB-1cjy: HUMAN CYTOSOLIC PHOSPHOLIPASE A2 -

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Basic information

Entry
Database: PDB / ID: 1cjy
TitleHUMAN CYTOSOLIC PHOSPHOLIPASE A2
ComponentsPROTEIN (CYTOSOLIC PHOSPHOLIPASE A2)
KeywordsHYDROLASE / PHOSPHOLIPASE / LIPID-BINDING
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 / glycerol metabolic process / arachidonic acid metabolic process / phosphatidylinositol-5-phosphate binding / positive regulation of T-helper 1 type immune response / phosphatidylcholine catabolic process / lysophospholipase activity / positive regulation of prostaglandin secretion / phospho-PLA2 pathway / calcium-dependent phospholipase A2 activity / COPI-independent Golgi-to-ER retrograde traffic / phosphatidylinositol-3-phosphate binding / positive regulation of macrophage activation / leukotriene biosynthetic process / calcium-dependent phospholipid binding / positive regulation of platelet activation / phosphatidylinositol-4-phosphate binding / phospholipase A2 activity / 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 / Cytosolic phospholipase A2 catalytic domain / Cytosolic phospholipase A2 catalytic domain / C2 domain / Acyl transferase/acyl hydrolase/lysophospholipase / C2 domain ...Lysophospholipase, catalytic domain / Cytosolic phospholipase A2, C2 domain / Lysophospholipase catalytic domain / PLA2c domain profile. / Cytoplasmic phospholipase A2, catalytic subunit / Cytosolic phospholipase A2 catalytic domain / Cytosolic phospholipase A2 catalytic domain / 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 / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Cytosolic phospholipase A2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsDessen, A. / Tang, J. / Schmidt, H. / Stahl, M. / Clark, J.D. / Seehra, J. / Somers, W.S.
CitationJournal: Cell(Cambridge,Mass.) / Year: 1999
Title: Crystal structure of human cytosolic phospholipase A2 reveals a novel topology and catalytic mechanism.
Authors: Dessen, A. / Tang, J. / Schmidt, H. / Stahl, M. / Clark, J.D. / Seehra, J. / Somers, W.S.
History
DepositionApr 20, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Apr 20, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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

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Assembly

Deposited unit
A: PROTEIN (CYTOSOLIC PHOSPHOLIPASE A2)
B: PROTEIN (CYTOSOLIC PHOSPHOLIPASE A2)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,1708
Polymers170,6192
Non-polymers5516
Water1,04558
1
A: PROTEIN (CYTOSOLIC PHOSPHOLIPASE A2)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,5854
Polymers85,3101
Non-polymers2753
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PROTEIN (CYTOSOLIC PHOSPHOLIPASE A2)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,5854
Polymers85,3101
Non-polymers2753
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)153.590, 95.490, 139.130
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein PROTEIN (CYTOSOLIC PHOSPHOLIPASE A2) / CPLA2


Mass: 85309.734 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P47712, phospholipase A2
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 58 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.99 Å3/Da / Density % sol: 58.84 %
Crystal growpH: 8.5 / Details: pH 8.5
Crystal
*PLUS
Density % sol: 60 %
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 6.2 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.1 MMES1drop
230 mMspermidine1drop
38 %PEG10001drop
413 %DMSO1drop
512 mg/mlprotain1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.2, 1.6496
DetectorType: ADSC / Detector: CCD / Date: Mar 1, 1998
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.21
21.64961
ReflectionResolution: 2.5→12 Å / Num. obs: 66223 / % possible obs: 93.3 % / Redundancy: 4.1 % / Rsym value: 0.064 / Net I/σ(I): 18.2
Reflection
*PLUS
Num. measured all: 271686 / Rmerge(I) obs: 0.064
Reflection shell
*PLUS
% possible obs: 87.9 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 3.3

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Processing

Software
NameVersionClassification
SHARPphasing
X-PLOR3.843refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.5→12 Å / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.298 -10 %RANDOM
Rwork0.229 ---
obs0.229 66223 93.3 %-
Refinement stepCycle: LAST / Resolution: 2.5→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9620 0 28 58 9706
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.016
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.94
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.843 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 12 Å / σ(F): 2 / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 47.7 Å2

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