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- PDB-1w52: Crystal structure of a proteolyzed form of pancreatic lipase rela... -

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Basic information

Entry
Database: PDB / ID: 1w52
TitleCrystal structure of a proteolyzed form of pancreatic lipase related protein 2 from horse
ComponentsPANCREATIC LIPASE RELATED PROTEIN 2
KeywordsLIPASE / PANCREATIC LIPASE RELATED PROTEINS / DETERGENT / CLEAVED FLAP
Function / homology
Function and homology information


galactolipase / zymogen granule membrane / triacylglycerol lipase / triacylglycerol lipase activity / lipid catabolic process / neuron projection / extracellular region / metal ion binding
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. / 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
DECYLAMINE-N,N-DIMETHYL-N-OXIDE / Pancreatic lipase-related protein 2
Similarity search - Component
Biological speciesEQUUS CABALLUS (horse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.99 Å
AuthorsMancheno, J.M. / Jayne, S. / Kerfelec, B. / Chapus, C. / Crenon, I. / Hermoso, J.A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2004
Title: Crystalization of a Proteolyzed Form of the Horse Pancreatic Lipase-Related Protein 2: Structural Basis for the Specific Detergent Requirement.
Authors: Mancheno, J.M. / Jayne, S. / Kerfelec, B. / Chapus, C. / Crenon, I. / Hermoso, J.A.
History
DepositionAug 4, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 12, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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_database_status.status_code_sf / _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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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 1.4Nov 6, 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
X: PANCREATIC LIPASE RELATED PROTEIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,5985
Polymers50,1151
Non-polymers4834
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)128.426, 128.426, 85.818
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein PANCREATIC LIPASE RELATED PROTEIN 2


Mass: 50114.840 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) EQUUS CABALLUS (horse) / Organ: PANCREAS / References: UniProt: Q95KP4
#2: Chemical ChemComp-DDQ / DECYLAMINE-N,N-DIMETHYL-N-OXIDE


Mass: 201.349 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H27NO
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
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: 4.08 Å3/Da / Density % sol: 70 %
Crystal growpH: 8.5 / Details: pH 8.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 4, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.99→46 Å / Num. obs: 16857 / % possible obs: 100 % / Redundancy: 13.6 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 5.4
Reflection shellResolution: 2.99→3.15 Å / Redundancy: 12.2 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 1.6 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
SCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BU8

1bu8


Resolution: 2.99→26.17 Å / Cor.coef. Fo:Fc: 0.892 / Cor.coef. Fo:Fc free: 0.838 / SU B: 17.505 / SU ML: 0.313 / Cross valid method: THROUGHOUT / ESU R: 0.968 / ESU R Free: 0.42 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. CHAINS FROM SEVERAL SEQUENCE REGIONS FROM THE C-TERMINAL DOMAIN ARE NOT DEFINED IN THE ELECTRON DENSITY MAP THE FOLLOWING REGIONS ARE NOT ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. CHAINS FROM SEVERAL SEQUENCE REGIONS FROM THE C-TERMINAL DOMAIN ARE NOT DEFINED IN THE ELECTRON DENSITY MAP THE FOLLOWING REGIONS ARE NOT DEFINED IN ELECTRON DENSITY MAP, 346-354,363-368,379-386,398-402,407-424,433-452 B- FACTORS OF THESE RESIDUES HAVE BEEN CHANGED TOP 100.00
RfactorNum. reflection% reflectionSelection details
Rfree0.294 847 5 %RANDOM
Rwork0.231 ---
obs0.234 15958 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 52.09 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20.01 Å20 Å2
2--0.02 Å20 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 2.99→26.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3494 0 30 0 3524
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0213611
X-RAY DIFFRACTIONr_bond_other_d0.0020.023129
X-RAY DIFFRACTIONr_angle_refined_deg1.9931.9514891
X-RAY DIFFRACTIONr_angle_other_deg1.36837337
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5495446
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0970.2515
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024045
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02729
X-RAY DIFFRACTIONr_nbd_refined0.2660.21012
X-RAY DIFFRACTIONr_nbd_other0.2620.24070
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0930.22082
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1940.291
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1730.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3690.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3290.244
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2810.21
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7651.52222
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.48723576
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.50231389
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it6.1634.51315
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.99→3.07 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.421 65
Rwork0.342 1155

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