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- PDB-2oxe: Structure of the Human Pancreatic Lipase-related Protein 2 -

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Basic information

Entry
Database: PDB / ID: 2oxe
TitleStructure of the Human Pancreatic Lipase-related Protein 2
ComponentsPancreatic lipase-related protein 2
KeywordsHYDROLASE / Glycoprotein / Lipid degradation / Pancreatic Lipase / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


galactolipase / galactolipid catabolic process / galactolipase activity / 1-18:1-2-16:0-monogalactosyldiacylglycerol lipase activity / Digestion of dietary lipid / lipid digestion / triglyceride catabolic process / phospholipase activity / monoacylglycerol lipase activity / zymogen granule membrane ...galactolipase / galactolipid catabolic process / galactolipase activity / 1-18:1-2-16:0-monogalactosyldiacylglycerol lipase activity / Digestion of dietary lipid / lipid digestion / triglyceride catabolic process / phospholipase activity / monoacylglycerol lipase activity / zymogen granule membrane / phospholipid catabolic process / phosphatidylcholine catabolic process / triacylglycerol lipase / triacylglycerol lipase activity / triglyceride metabolic process / neuron projection / calcium ion binding / extracellular space / extracellular region
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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsWalker, J.R. / Davis, T. / Seitova, A. / Finerty Jr., P.J. / Butler-Cole, C. / Kozieradzki, I. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C.H. / Edwards, A.M. ...Walker, J.R. / Davis, T. / Seitova, A. / Finerty Jr., P.J. / Butler-Cole, C. / Kozieradzki, I. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Dhe-Paganon, S. / Structural Genomics Consortium (SGC)
Citation
Journal: Biochemistry / Year: 2008
Title: Structure of human pancreatic lipase-related protein 2 with the lid in an open conformation.
Authors: Eydoux, C. / Spinelli, S. / Davis, T.L. / Walker, J.R. / Seitova, A. / Dhe-Paganon, S. / De Caro, A. / Cambillau, C. / Carriere, F.
#1: Journal: Biochemistry / Year: 2004
Title: Human Pancreatic Lipase-Related Protein 2 Is a Galactolipase
Authors: Sias, B. / Ferrato, F. / Grandval, P. / Lafont, D. / Boullanger, P. / De Caro, A. / Leboeuf, B. / Verger, R. / Carriere, F.
#2: Journal: J.Biol.Chem. / Year: 1992
Title: Two Novel Human Pancreatic Lipase Related Proteins, hPLRP1 and hPLRP2
Authors: Giller, T. / Buchwald, P. / Blum-Kaelin, D. / Hunziker, W.
History
DepositionFeb 20, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_validate_chiral / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _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.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_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 / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 30, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pancreatic lipase-related protein 2
B: Pancreatic lipase-related protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,91511
Polymers103,8362
Non-polymers2,0799
Water1,36976
1
A: Pancreatic lipase-related protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,9405
Polymers51,9181
Non-polymers1,0224
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Pancreatic lipase-related protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,9756
Polymers51,9181
Non-polymers1,0575
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)216.922, 216.922, 123.618
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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Components

#1: Protein Pancreatic lipase-related protein 2


Mass: 51918.004 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue: Pancreas / Gene: PNLIPRP2, PLRP2 / Plasmid: pAB-Bee / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): High5 / References: UniProt: P54317, triacylglycerol lipase
#2: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2-2-2/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / Source method: isolated from a natural source / Formula: H2O

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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: 3.5 Å3/Da / Density % sol: 64.85 %
Crystal growTemperature: 298 K / pH: 5.5
Details: 1.17M Ammonium sulfate, 0.1M Sodium cacodylate pH 5.5, 0.04M NaCl, cryoprotected with 15% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 5.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 19, 2006
RadiationMonochromator: SAGITALLY FOCUSED SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. obs: 36137 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Rsym value: 0.092 / Net I/σ(I): 12.7
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 2.76 / Rsym value: 0.785 / % possible all: 99.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BU8

1bu8


Resolution: 2.8→29.88 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.911 / SU B: 33.297 / SU ML: 0.314 / Cross valid method: THROUGHOUT / ESU R: 0.641 / ESU R Free: 0.334 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS
RfactorNum. reflection% reflectionSelection details
Rfree0.26093 1811 5 %RANDOM
Rwork0.22228 ---
obs0.22432 34305 99.27 %-
all-36116 --
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: 39.618 Å2
Baniso -1Baniso -2Baniso -3
1-4.11 Å20 Å20 Å2
2--4.11 Å20 Å2
3----8.22 Å2
Refinement stepCycle: LAST / Resolution: 2.8→29.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6642 0 129 76 6847
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0226997
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1421.9639525
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2755868
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.63524.587327
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.52151045
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.81531
X-RAY DIFFRACTIONr_chiral_restr0.0780.21034
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.025401
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2010.23124
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3070.24783
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1330.2221
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0920.25
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1690.249
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0790.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3221.54404
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.58526915
X-RAY DIFFRACTIONr_scbond_it0.88532925
X-RAY DIFFRACTIONr_scangle_it1.654.52610
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.872 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.443 122 -
Rwork0.338 2464 -
obs--98.63 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.0568-0.8243-0.18662.5774-0.34651.62490.2684-0.1971-0.0033-0.1005-0.19280.11990.378-0.01-0.07560.24290.04570.01870.19120.0940.187815.753-16.25950.298
22.79092.38331.9153.23264.192111.79350.39-0.598-0.63970.0637-0.028-0.72581.24550.9978-0.3620.30340.49090.0950.26360.1230.384636.716-24.92350.366
32.257-0.42560.32451.61080.54981.737-0.09130.0174-0.0524-0.2257-0.0428-0.26880.52140.34870.13410.18830.18940.12570.28390.12970.298628.668-14.51946.174
41.92330.81570.35791.85640.18733.54260.06430.0856-0.164-0.1610.08570.0301-0.16140.1224-0.150.10170.06090.08830.25470.01220.378921.547-3.98951.093
51.5521.2982-2.21513.55-0.02654.51520.0184-0.23680.52690.004-0.01430.4057-0.586-0.3264-0.00410.10660.04510.16450.22490.05440.457423.4273.84943.195
60.61090.7994-1.14893.37250.2075.19120.25720.43920.3579-0.5727-0.2579-0.0339-0.04980.22110.00070.09840.10410.18180.23250.08940.418230.3920.24334.359
73.02252.8303-0.05539.2111-2.38769.52320.2384-0.44340.9962-0.174-0.0351-0.2819-1.2440.1058-0.20330.071-0.0720.36340.1798-0.04120.506934.85315.47140.113
82.86582.2704-2.38641.9236-2.23842.95550.3708-0.33010.55110.0438-0.171-0.3255-0.3630.4278-0.19980.07-0.00650.24290.27130.02070.547637.779.82238.601
914.1182-2.2561-3.470414.90092.30675.7730.24460.94480.9263-0.4840.34990.6312-0.7164-0.3641-0.59450.07-0.06010.35430.11270.13950.377743.46521.48919.182
106.06393.1134-4.38645.8218-4.266.28320.3189-0.05771.0425-0.19040.35650.1671-0.3056-0.2934-0.67550.0406-0.0550.30780.07930.0190.573648.68122.67923.451
113.7150.11480.01317.09380.33341.4876-0.19650.2529-0.1019-0.6480.06340.1155-0.2393-0.64110.13310.33850.121-0.19720.2605-0.0710.0586-17.97313.42913.012
129.12234.2343-8.4868.7586-8.607314.1609-0.55741.17031.3852-0.72670.97580.8889-1.1151-1.8979-0.41830.38490.37-0.35990.27330.01010.5461-23.5635.15311.929
132.99550.99910.45962.09831.41472.4803-0.20560.16230.1988-0.0950.03230.2632-0.4762-0.52470.17320.36080.1913-0.15960.1744-0.03850.225-14.66825.65717.185
140.38520.4162-0.0947.06070.42986.638-0.04720.2286-0.1347-0.52160.0490.0453-0.02870.1465-0.00180.3142-0.0019-0.0570.1427-0.09450.2357-4.77317.18712.826
152.17371.5172-1.17043.93930.25652.5598-0.25290.0487-0.3415-0.16930.1054-0.5748-0.18810.15060.14750.25690.029-0.02990.136-0.07280.31362.88618.20522.316
160.44620.3687-0.61771.4102-0.05591.04180.1273-0.41840.18780.22-0.09940.272-0.4351-0.124-0.02790.42010.0482-0.08660.1585-0.07420.3323-1.16626.64729.457
178.87740.64512.07781.6739-3.45718.4874-0.31650.4260.0903-0.4771-0.1875-0.9723-0.41951.27710.50410.3849-0.2010.01510.0869-0.15620.411515.76528.07124.954
183.02571.67572.16661.63282.25643.1353-0.21050.24750.2822-0.34970.3449-0.32-0.45950.5299-0.13440.459-0.07480.01450.0047-0.08580.325310.15531.80126.202
197.9036-2.36863.15227.1360.80511.22340.0502-1.223-0.10910.79160.2052-0.15620.7032-0.4561-0.25530.1839-0.019-0.0458-0.0678-0.15980.438320.98736.65446.489
205.81070.77663.20483.30793.80975.6235-0.2419-0.28590.209-0.11540.4869-0.41070.12140.2969-0.2450.1273-0.04210.00420.0535-0.23690.448922.50741.64641.96
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA18 - 633 - 48
2X-RAY DIFFRACTION2AA64 - 8649 - 71
3X-RAY DIFFRACTION3AA87 - 17272 - 157
4X-RAY DIFFRACTION4AA173 - 212158 - 197
5X-RAY DIFFRACTION5AA213 - 249198 - 234
6X-RAY DIFFRACTION6AA250 - 303235 - 288
7X-RAY DIFFRACTION7AA304 - 327289 - 312
8X-RAY DIFFRACTION8AA328 - 366313 - 351
9X-RAY DIFFRACTION9AA367 - 397352 - 382
10X-RAY DIFFRACTION10AA398 - 469383 - 454
11X-RAY DIFFRACTION11BB18 - 633 - 48
12X-RAY DIFFRACTION12BB64 - 8649 - 71
13X-RAY DIFFRACTION13BB87 - 17272 - 157
14X-RAY DIFFRACTION14BB173 - 212158 - 197
15X-RAY DIFFRACTION15BB213 - 253198 - 238
16X-RAY DIFFRACTION16BB254 - 303239 - 288
17X-RAY DIFFRACTION17BB304 - 327289 - 312
18X-RAY DIFFRACTION18BB328 - 366313 - 351
19X-RAY DIFFRACTION19BB367 - 398352 - 383
20X-RAY DIFFRACTION20BB399 - 469384 - 454

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