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- PDB-1bu8: RAT PANCREATIC LIPASE RELATED PROTEIN 2 -

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Basic information

Entry
Database: PDB / ID: 1bu8
TitleRAT PANCREATIC LIPASE RELATED PROTEIN 2
ComponentsPROTEIN (PANCREATIC LIPASE RELATED PROTEIN 2)
KeywordsHYDROLASE / LIPID DEGRADATION / PANCREATIC LIPASE
Function / homology
Function and homology information


intestinal lipid catabolic process / Digestion of dietary lipid / galactolipid catabolic process / galactolipase activity / galactolipase / phospholipase activity / triglyceride catabolic process / zymogen granule membrane / monoacylglycerol lipase activity / lipase activity ...intestinal lipid catabolic process / Digestion of dietary lipid / galactolipid catabolic process / galactolipase activity / galactolipase / phospholipase activity / triglyceride catabolic process / zymogen granule membrane / monoacylglycerol lipase activity / lipase activity / triacylglycerol lipase / triacylglycerol lipase activity / phospholipid catabolic process / phosphatidylcholine catabolic process / response to food / response to lipid / cellular defense response / response to glucocorticoid / phospholipid metabolic process / post-embryonic development / response to bacterium / response to peptide hormone / neuron projection / calcium ion binding / extracellular space
Similarity search - Function
Pancreatic lipase / Lipase, LIPH-type / Lipase, N-terminal / Triacylglycerol lipase family / Lipase / Lipase / PLAT/LH2 domain / Lipoxygenase-1 / Lipoxygenase homology 2 (beta barrel) domain / PLAT/LH2 domain ...Pancreatic lipase / Lipase, LIPH-type / Lipase, N-terminal / Triacylglycerol lipase family / Lipase / Lipase / PLAT/LH2 domain / Lipoxygenase-1 / Lipoxygenase homology 2 (beta barrel) domain / PLAT/LH2 domain / PLAT/LH2 domain superfamily / PLAT/LH2 domain / PLAT domain profile. / Lipases, serine active site. / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Pancreatic lipase-related protein 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsRoussel, A. / Cambillau, C.
CitationJournal: J.Biol.Chem. / Year: 1998
Title: Structure and activity of rat pancreatic lipase-related protein 2.
Authors: Roussel, A. / Yang, Y. / Ferrato, F. / Verger, R. / Cambillau, C. / Lowe, M.
History
DepositionSep 14, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Dec 23, 1998Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (PANCREATIC LIPASE RELATED PROTEIN 2)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1422
Polymers50,9201
Non-polymers2211
Water5,314295
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.393, 79.133, 60.940
Angle α, β, γ (deg.)90.00, 102.07, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein PROTEIN (PANCREATIC LIPASE RELATED PROTEIN 2)


Mass: 50920.418 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Organ: PANCREAS / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P54318, triacylglycerol lipase
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 295 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.66 Å3/Da / Density % sol: 54 %
Crystal growpH: 8.4
Details: PROTEIN WAS CRYSTALLIZED FROM 8% PEG 8000 WITH 0.1 M TRIS/HCL PH 8.4
Crystal
*PLUS
Density % sol: 54 %
Crystal grow
*PLUS
pH: 8.5 / Method: vapor diffusion, hanging drop / Details: used to seeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
118 mg/mlprotein1drop
20.2 M1dropNaCl
30.1 MTris-HCl1drop
48 %PEG80001reservoir
50.1 MTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.97
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 15, 1997 / Details: MIRRORS
RadiationMonochromator: LURE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.8→10 Å / Num. obs: 47899 / % possible obs: 97.5 % / Observed criterion σ(I): 1.5 / Redundancy: 2.4 % / Rmerge(I) obs: 0.063 / Rsym value: 0.063 / Net I/σ(I): 9.1
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 2.3 / Rsym value: 0.42 / % possible all: 81.9
Reflection shell
*PLUS
% possible obs: 81.9 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLOR3.843refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1THG

1thg


Resolution: 1.8→10 Å / Data cutoff high absF: 750 / Data cutoff low absF: 50 / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.244 1626 5 %RANDOM
Rwork0.202 ---
obs0.202 36060 97.3 %-
Displacement parametersBiso mean: 20.78 Å2
Refinement stepCycle: LAST / Resolution: 1.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3518 0 14 295 3827
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
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_deg1.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.5
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.3
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
LS refinement shellResolution: 1.8→1.83 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.2763 42 5 %
Rwork0.1774 792 -
obs--81.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19X.PROTOPH19X.PRO
X-RAY DIFFRACTION2PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION3PARAM3_MOD.CHOTOPH3.CHO
Software
*PLUS
Name: X-PLOR / Version: 3.843 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 10 Å / σ(F): 2 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.5
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.3
LS refinement shell
*PLUS
% reflection Rfree: 5 %

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