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- PDB-1k8q: CRYSTAL STRUCTURE OF DOG GASTRIC LIPASE IN COMPLEX WITH A PHOSPHO... -

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Basic information

Entry
Database: PDB / ID: 1k8q
TitleCRYSTAL STRUCTURE OF DOG GASTRIC LIPASE IN COMPLEX WITH A PHOSPHONATE INHIBITOR
ComponentsTriacylglycerol lipase, gastric
KeywordsHYDROLASE / APHA BETA HYDROLASE FOLD
Function / homology
Function and homology information


triacylglycerol lipase / triacylglycerol lipase activity / lipid catabolic process / intracellular membrane-bounded organelle / extracellular region
Similarity search - Function
Lipase, eukaryotic / Lipases, serine active site. / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
UNDECYL-PHOSPHINIC ACID BUTYL ESTER / Gastric triacylglycerol lipase
Similarity search - Component
Biological speciesCanis lupus familiaris (dog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsRoussel, A. / Miled, N. / Berti-Dupuis, L. / Riviere, M. / Spinelli, S. / Berna, P. / Gruber, V. / Verger, R. / Cambillau, C.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: Crystal structure of the open form of dog gastric lipase in complex with a phosphonate inhibitor.
Authors: Roussel, A. / Miled, N. / Berti-Dupuis, L. / Riviere, M. / Spinelli, S. / Berna, P. / Gruber, V. / Verger, R. / Cambillau, C.
History
DepositionOct 25, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Aug 16, 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 13, 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: Triacylglycerol lipase, gastric
B: Triacylglycerol lipase, gastric
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,77514
Polymers85,8682
Non-polymers2,90712
Water6,882382
1
A: Triacylglycerol lipase, gastric
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,3877
Polymers42,9341
Non-polymers1,4546
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Triacylglycerol lipase, gastric
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,3877
Polymers42,9341
Non-polymers1,4546
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.209, 164.498, 177.156
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Triacylglycerol lipase, gastric


Mass: 42933.855 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Canis lupus familiaris (dog) / Species: Canis lupus / Strain: familiaris / Gene: LIPF / Plasmid: pUC18 / Production host: Zea mays (maize) / Strain (production host): Hi-II maize germplasm / References: UniProt: P80035, 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.: 8
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: Sugar ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#4: Chemical ChemComp-C11 / UNDECYL-PHOSPHINIC ACID BUTYL ESTER


Mass: 276.395 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H33O2P
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 382 / 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: 2.6 Å3/Da / Density % sol: 52.61 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 30 % PEGMME 2000, 0.1 M sodium acetate and 0.2 M ammonium sulfate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
130 %PEG2000 MME1reservoir
20.1 Msodium acetate1reservoir
30.2 Mammonium sulfate1reservoirpH4.6
45 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.979 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 27, 2000
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.7→40 Å / Num. all: 25123 / Num. obs: 24343 / % possible obs: 97.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.058
Reflection shellResolution: 2.7→2.75 Å / Rmerge(I) obs: 0.215 / % possible all: 88.7
Reflection
*PLUS
Lowest resolution: 40 Å / Redundancy: 3 %
Reflection shell
*PLUS
% possible obs: 97.5 % / Redundancy: 2.2 % / Rmerge(I) obs: 0.212 / Mean I/σ(I) obs: 1.8

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALAdata scaling
AMoREphasing
CNS1refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HLG

1hlg


Resolution: 2.7→15 Å / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2572 1174 RANDOM
Rwork0.1965 --
all-24902 -
obs-24389 -
Refinement stepCycle: LAST / Resolution: 2.7→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6064 0 188 382 6634
Refinement
*PLUS
Lowest resolution: 15 Å / σ(F): 1 / % reflection Rfree: 5 % / Rfactor obs: 0.192 / Rfactor Rfree: 0.258
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.0086
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_deg1.5

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