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- PDB-2pvs: Structure of human pancreatic lipase related protein 2 mutant N336Q -

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Basic information

Entry
Database: PDB / ID: 2pvs
TitleStructure of human pancreatic lipase related protein 2 mutant N336Q
ComponentsPancreatic lipase-related protein 2
KeywordsHYDROLASE / Lipase / galacto lipids hydrolysis
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 / acylglycerol 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 / acylglycerol lipase activity / zymogen granule membrane / phospholipid catabolic process / phosphatidylcholine catabolic process / triacylglycerol lipase / triglyceride 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: 3 Å
AuthorsSpinelli, S. / Eydoux, C. / Carriere, F. / Cambillau, C.
CitationJournal: 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.
History
DepositionMay 10, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

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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)101,20912
Polymers100,3602
Non-polymers84910
Water1,20767
1
A: Pancreatic lipase-related protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,7017
Polymers50,1801
Non-polymers5206
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Pancreatic lipase-related protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,5085
Polymers50,1801
Non-polymers3284
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Pancreatic lipase-related protein 2
B: Pancreatic lipase-related protein 2
hetero molecules

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

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

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


Theoretical massNumber of molelcules
Total (without water)404,83648
Polymers401,4418
Non-polymers3,39540
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_457y-1/2,x+1/2,-z+5/21
crystal symmetry operation10_565-x,-y+1,z1
crystal symmetry operation16_557-y+1/2,-x+1/2,-z+5/21
Buried area22220 Å2
ΔGint-648.6 kcal/mol
Surface area134290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)216.181, 216.181, 123.672
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B

NCS domain segments:

Component-ID: 1 / Refine code: 5

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11VALVALPROPROAA1 - 2353 - 237
21VALVALPROPROBB1 - 2353 - 237
12ILEILEALAALAAA255 - 320257 - 322
22ILEILEALAALABB255 - 320257 - 322

NCS ensembles :
ID
1
2

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Components

#1: Protein Pancreatic lipase-related protein 2


Mass: 50180.184 Da / Num. of mol.: 2 / Mutation: N336Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PNLIPRP2, PLRP2 / Production host: Pichia pastoris (fungus) / Strain (production host): SMD 1168 / References: UniProt: P54317, triacylglycerol lipase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 3.6 Å3/Da / Density % sol: 65.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.7
Details: 6 microliter of protein (14.5 mg/ml in 0.2 M NaCl, 25 mM Tris-HCl, pH 8.0) and 2 microliter of 2.05 M Ammonium sulphate, 0.1 M Hepes, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 9, 2007 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 3→35 Å / Num. all: 27791 / Num. obs: 27791 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6 % / Biso Wilson estimate: 88 Å2 / Rmerge(I) obs: 0.118 / Rsym value: 0.118 / Net I/σ(I): 10.5
Reflection shellResolution: 3→3.16 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 1.5 / Num. unique all: 4339 / Rsym value: 0.48 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQuantumdata collection
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1GPL

1gpl


Resolution: 3→34.18 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.888 / SU B: 31.566 / SU ML: 0.279 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.383 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24948 1477 5 %RANDOM
Rwork0.18966 ---
obs0.1926 27791 99.22 %-
all-27791 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 51.447 Å2
Baniso -1Baniso -2Baniso -3
1-2.43 Å20 Å20 Å2
2--2.43 Å20 Å2
3----4.86 Å2
Refine analyzeLuzzati coordinate error free: 0.38 Å
Refinement stepCycle: LAST / Resolution: 3→34.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6868 0 42 67 6977
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0227078
X-RAY DIFFRACTIONr_bond_other_d0.0040.024827
X-RAY DIFFRACTIONr_angle_refined_deg1.3691.9539586
X-RAY DIFFRACTIONr_angle_other_deg0.883.00411722
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4975873
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.0524.732336
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.065151154
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.711530
X-RAY DIFFRACTIONr_chiral_restr0.0790.21003
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.027926
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021436
X-RAY DIFFRACTIONr_nbd_refined0.2270.21656
X-RAY DIFFRACTIONr_nbd_other0.1980.25155
X-RAY DIFFRACTIONr_nbtor_refined0.190.23423
X-RAY DIFFRACTIONr_nbtor_other0.0890.23819
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1740.2181
X-RAY DIFFRACTIONr_metal_ion_refined0.1560.26
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1880.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2080.227
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.330.22
X-RAY DIFFRACTIONr_mcbond_it0.4961.54503
X-RAY DIFFRACTIONr_mcbond_other0.0781.51794
X-RAY DIFFRACTIONr_mcangle_it0.85427010
X-RAY DIFFRACTIONr_scbond_it1.07132985
X-RAY DIFFRACTIONr_scangle_it1.764.52576
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-IDNumberTypeRms dev position (Å)Weight position
11374medium positional0.160.5
2384medium positional0.190.5
11730loose positional0.535
2496loose positional0.45
11374medium thermal0.472
2384medium thermal0.362
11730loose thermal1.0610
2496loose thermal0.7210
LS refinement shellResolution: 3→3.077 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.376 118 -
Rwork0.287 1993 -
obs--99.95 %

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