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- PDB-1bvm: SOLUTION NMR STRUCTURE OF BOVINE PANCREATIC PHOSPHOLIPASE A2, 20 ... -

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Entry
Database: PDB / ID: 1bvm
TitleSOLUTION NMR STRUCTURE OF BOVINE PANCREATIC PHOSPHOLIPASE A2, 20 STRUCTURES
ComponentsPROTEIN (PHOSPHOLIPASE A2)
KeywordsHYDROLASE / PHOSPHOLIPASE A2
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 / calcium-dependent phospholipase A2 activity ...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 / calcium-dependent phospholipase A2 activity / 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)
MethodSOLUTION NMR / simulated annealing
AuthorsYuan, C.-H. / Byeon, I.-J.L. / Li, Y. / Tsai, M.-D.
CitationJournal: Biochemistry / Year: 1999
Title: Structural analysis of phospholipase A2 from functional perspective. 1. Functionally relevant solution structure and roles of the hydrogen-bonding network.
Authors: Yuan, C. / Byeon, I.J. / Li, Y. / Tsai, M.D.
History
DepositionSep 14, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Sep 16, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Dec 27, 2023Group: 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: PROTEIN (PHOSPHOLIPASE A2)


Theoretical massNumber of molelcules
Total (without water)13,8111
Polymers13,8111
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 40CLOSEST TO THE MEAN STRUCTURE WHICH SHOWS LITTLE RESTRAINT VIOLATION
Representative

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Components

#1: Protein PROTEIN (PHOSPHOLIPASE A2)


Mass: 13810.504 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Description: BOVINE PANCREAS / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)[PLYSS] / References: UniProt: P00593, phospholipase A2
Sequence detailsSEE NOEL, J. P. ET AL.(1989) J. CELL. BIOCHEM. 40, 309-320.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D COSY
1212D TOCSY
1312D NOESY
1413D HN(CA)CB
1513D HNCA
1613D CBCA(CO)NH
1713D HN(CO)CA
1813D HNHA
1913D HNHB
110115N-EDITED NOESY-HSQC
111115N-EDITED TOCSY-HSQC
112113C-EDITED NOESY-HMQC
1131AND 13C-EDITED (H)CCH-TOCSY
NMR detailsText: THE SOLUTION STRUCTURE OF THE BOVINE PANCREATIC PHOSPHOLIPASE A2 HAS BEEN DETERMINED BY MULTI-DIMENSIONAL HETERONUCLEAR NMR. THE STRUCTURES WERE CALCULATED USING THE SIMULATED ANNEALING ...Text: THE SOLUTION STRUCTURE OF THE BOVINE PANCREATIC PHOSPHOLIPASE A2 HAS BEEN DETERMINED BY MULTI-DIMENSIONAL HETERONUCLEAR NMR. THE STRUCTURES WERE CALCULATED USING THE SIMULATED ANNEALING PROTOCOL OF NILGES ET AL. (1988) FEBS LETT. 229, 129-136 USING THE PROGRAM X-PLOR 3.1 (BRUNGER). THE CALCULATION IS BASED ON 1937 EXPERIMENTAL NMR RESTRAINTS (1823 DISTANCE AND 114 -RSION ANGLE RESTRAINTS).

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Sample preparation

DetailsContents: H2O AND D2O, 50 MM CACL2, 300 MM NACL
Sample conditionsIonic strength: 300 mM NACL, 50 mM CACL2 / pH: 6.0 / Temperature: 310 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMX 600BrukerDMX 6006001
Bruker DRX 800BrukerDRX 8008002

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Processing

NMR software
NameDeveloperClassification
X-PLORBRUNGERrefinement
X-PLORstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
NMR ensembleConformer selection criteria: CLOSEST TO THE MEAN STRUCTURE WHICH SHOWS LITTLE RESTRAINT VIOLATION
Conformers calculated total number: 40 / Conformers submitted total number: 20

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