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- PDB-4bp2: CRYSTALLOGRAPHIC REFINEMENT OF BOVINE PRO-PHOSPHOLIPASE A2 AT 1.6... -

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Basic information

Entry
Database: PDB / ID: 4bp2
TitleCRYSTALLOGRAPHIC REFINEMENT OF BOVINE PRO-PHOSPHOLIPASE A2 AT 1.6 ANGSTROMS RESOLUTION
ComponentsPHOSPHOLIPASE A2
KeywordsCARBOXYLIC ESTER HYDROLASE ZYMOGEN
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 / bile acid binding ...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 / bile acid binding / phospholipase A2 / calcium-dependent phospholipase A2 activity / arachidonate secretion / lipid catabolic process / innate immune response in mucosa / phospholipid binding / positive regulation of fibroblast proliferation / antimicrobial humoral immune response mediated by antimicrobial peptide / 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 / Resolution: 1.6 Å
AuthorsFinzel, B.C. / Weber, P.C. / Ohlendorf, D.H. / Salemme, F.R.
CitationJournal: Acta Crystallogr.,Sect.B / Year: 1991
Title: Crystallographic refinement of bovine pro-phospholipase A2 at 1.6 A resolution.
Authors: Finzel, B.C. / Weber, P.C. / Ohlendorf, D.H. / Salemme, F.R.
History
DepositionSep 7, 1990Processing site: BNL
Revision 1.0Oct 15, 1991Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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_entry_details.has_protein_modification / _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: PHOSPHOLIPASE A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,8154
Polymers14,5381
Non-polymers2763
Water1,08160
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.950, 46.950, 102.000
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Atom site foot note1: ELECTRON DENSITY IS POOR FOR RESIDUES ALA 1, LEU 2, TRP 3, CYS 61, LYS 62, VAL 63, LEU 64, ASN 71 AND ASN 72 AND THE COORDINATES FOR THESE REGIONS SHOULD NOT BE CONSIDERED RELIABLE.
2: ONLY CALCIUM ION 201 WAS FOUND IN THE PROTEIN.

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Components

#1: Protein PHOSPHOLIPASE A2


Mass: 14538.293 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / References: UniProt: P00593, phospholipase A2
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsTWO MOLECULES OF THE PRECIPITATING AGENT, 2-METHYL-2,4-PENTANEDIOL, ARE INCLUDED IN THE MODEL.
Sequence detailsZYMOGEN HAS FOUR EXTRA RESIDUES AT THE AMINO TERMINUS COMPARED WITH MATURE PHOSPHOLIPASE. THESE ...ZYMOGEN HAS FOUR EXTRA RESIDUES AT THE AMINO TERMINUS COMPARED WITH MATURE PHOSPHOLIPASE. THESE RESIDUES ARE NOT SEEN IN THE ELECTRON DENSITY MAP. RESIDUE NUMBERING IS THUS THE SAME AS IN THE MATURE ENZYME.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.23 Å3/Da / Density % sol: 44.88 %
Crystal grow
*PLUS
Method: unknown / pH: 7.2 / Details: Drenth, J., (1976) Nature(London), 264, 373.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
2enzyme11
10.05 MTris maleate11
35 mM11CaCl2
475 %(v/v)MPD11

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.5 Å / Num. all: 18736 / Num. obs: 17470 / Num. measured all: 88408 / Rmerge(I) obs: 0.054

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 1.6→5 Å
Details: ELECTRON DENSITY IS POOR FOR RESIDUES ALA 1, LEU 2, TRP 3, CYS 61, LYS 62, VAL 63, LEU 64, ASN 71 AND ASN 72 AND THE COORDINATES FOR THESE REGIONS SHOULD NOT BE CONSIDERED RELIABLE.
RfactorNum. reflection
obs0.19 14100
Refinement stepCycle: LAST / Resolution: 1.6→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms895 0 1 76 972
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0240.03
X-RAY DIFFRACTIONp_angle_d0.0370.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0470.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.1031
X-RAY DIFFRACTIONp_mcangle_it1.962
X-RAY DIFFRACTIONp_scbond_it2.0461.5
X-RAY DIFFRACTIONp_scangle_it3.3063
X-RAY DIFFRACTIONp_plane_restr0.0170.03
X-RAY DIFFRACTIONp_chiral_restr0.2580.3
X-RAY DIFFRACTIONp_singtor_nbd0.1910.5
X-RAY DIFFRACTIONp_multtor_nbd0.210.5
X-RAY DIFFRACTIONp_xhyhbond_nbd0.2330.5
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Lowest resolution: 5 Å / Num. reflection obs: 14667 / σ(I): 0.1 / Rfactor obs: 0.194
Solvent computation
*PLUS
Displacement parameters
*PLUS

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