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- PDB-1bci: C2 DOMAIN OF CYTOSOLIC PHOSPHOLIPASE A2, NMR, MINIMIZED AVERAGE S... -

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Basic information

Entry
Database: PDB / ID: 1bci
TitleC2 DOMAIN OF CYTOSOLIC PHOSPHOLIPASE A2, NMR, MINIMIZED AVERAGE STRUCTURE
ComponentsCYTOSOLIC PHOSPHOLIPASE A2
KeywordsHYDROLASE / LIPID DEGRADATION / CYTOSOLIC PHOSPHOLIPASE A2 / CALCIUM-DEPENDENT LIPID BINDING / C2 DOMAIN / PHOSPHOCHOLINE
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)
MethodSOLUTION NMR / DISTANCE GEOMETRY, SIMULATED ANNEALING, RESTRAINED MOLECULAR DYNAMICS, ETC.
AuthorsXu, G.Y. / Mcdonagh, T. / Yu, H.A. / Nalefski, E.A. / Clark, J.D. / Cumming, D.A.
CitationJournal: J.Mol.Biol. / Year: 1998
Title: Solution structure and membrane interactions of the C2 domain of cytosolic phospholipase A2.
Authors: Xu, G.Y. / McDonagh, T. / Yu, H.A. / Nalefski, E.A. / Clark, J.D. / Cumming, D.A.
History
DepositionApr 30, 1998Processing site: BNL
Revision 1.0Nov 25, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_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
Revision 1.4May 22, 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: CYTOSOLIC PHOSPHOLIPASE A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,0513
Polymers15,9711
Non-polymers802
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 75VIOLATION: NOES<0.3 A, DIHEDRAL ANGLES<3 DEGREES
Representative

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Components

#1: Protein CYTOSOLIC PHOSPHOLIPASE A2 / CALB DOMAIN


Mass: 15971.113 Da / Num. of mol.: 1 / Fragment: C2 DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: PROPRIETARY STRAIN/GI400
Plasmid details: A CDNA FRAGMENT ENCODING AMINO ACIDS 1-138 OF HUMAN CYTOSOLIC PHOSPHOLIPASE A2 WAS SUBCLONED INTO THE NCOI/ECORI SITES OF THE VECTOR SUCH THAT THE 5' CODONS ENCODING THE N-TERMINAL ...Plasmid details: A CDNA FRAGMENT ENCODING AMINO ACIDS 1-138 OF HUMAN CYTOSOLIC PHOSPHOLIPASE A2 WAS SUBCLONED INTO THE NCOI/ECORI SITES OF THE VECTOR SUCH THAT THE 5' CODONS ENCODING THE N-TERMINAL POLYHIS-TAG WERE REMOVED.
Plasmid: PTRCHISB(INVITROGEN) / Cell line (production host): PROPRIETARY STRAIN/GI400 / Production host: Escherichia coli (E. coli) / References: UniProt: P47712, phospholipase A2
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121TOCSY
NMR detailsText: N15-NOESY, HNHA-J, HNHB, CBCACONNH, HNCACB, HBHACONNH, HNHAHB, HCCH-TOCSY, LONG-RANGE-CCJ, CN-NOESY, ETC.

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Sample preparation

DetailsContents: 20 MM TRIS, 0.5MM CACL2
Sample conditionsIonic strength: 0.0 / pH: 7.1 / Pressure: 1 atm / Temperature: 308 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Varian UNIT+ / Manufacturer: Varian / Model: UNIT+ / Field strength: 600 MHz

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
NMR software
NameVersionDeveloperClassification
X-PLOR3.1BRUNGERrefinement
X-PLORstructure solution
RefinementMethod: DISTANCE GEOMETRY, SIMULATED ANNEALING, RESTRAINED MOLECULAR DYNAMICS, ETC.
Software ordinal: 1
Details: THIS AVERAGE-MINIMIZED STRUCTURE IS FROM 34 ENSEMBLE STRUCTURES, WHICH ARE BASED ON 2215 INTERPROTON DISTANCE RESTRAINTS DERIVED FROM NMR MEASUREMENTS INCLUDING 106 HYDROGEN BOND RESTRAINTS ...Details: THIS AVERAGE-MINIMIZED STRUCTURE IS FROM 34 ENSEMBLE STRUCTURES, WHICH ARE BASED ON 2215 INTERPROTON DISTANCE RESTRAINTS DERIVED FROM NMR MEASUREMENTS INCLUDING 106 HYDROGEN BOND RESTRAINTS AND 155 TORSION ANGLE RESTRAINTS. THE DETAILED ENERGETIC STATISTICS AND ATOMIC RMSD'S CAN BE FOUND IN THE J.MOL.BIOL CITATION.
NMR ensembleConformer selection criteria: VIOLATION: NOES<0.3 A, DIHEDRAL ANGLES<3 DEGREES / Conformers calculated total number: 75 / Conformers submitted total number: 1

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