[English] 日本語
Yorodumi
- PDB-1gpl: RP2 LIPASE -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1gpl
TitleRP2 LIPASE
ComponentsRP2 LIPASE
KeywordsSERINE ESTERASE / HYDROLASE / LIPID DEGRADATION / PANCREAS / GLYCOPROTEIN / CHIMERIC
Function / homology
Function and homology information


galactolipid catabolic process / galactolipase activity / positive regulation of triglyceride lipase activity / galactolipase / all-trans-retinyl-palmitate hydrolase, all-trans-retinol forming activity / lipoprotein lipase activity / Digestion of dietary lipid / phospholipase activity / triglyceride catabolic process / monoacylglycerol lipase activity ...galactolipid catabolic process / galactolipase activity / positive regulation of triglyceride lipase activity / galactolipase / all-trans-retinyl-palmitate hydrolase, all-trans-retinol forming activity / lipoprotein lipase activity / Digestion of dietary lipid / phospholipase activity / triglyceride catabolic process / monoacylglycerol lipase activity / zymogen granule membrane / lipase activity / intestinal cholesterol absorption / triacylglycerol lipase / triacylglycerol lipase activity / phospholipid catabolic process / Retinoid metabolism and transport / lipid catabolic process / phospholipid metabolic process / lipid metabolic process / neuron projection / calcium ion binding / extracellular space / 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. / 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 triacylglycerol lipase / Pancreatic lipase-related protein 2
Similarity search - Component
Biological speciesCavia porcellus (domestic guinea pig)
MethodX-RAY DIFFRACTION / Resolution: 2.01 Å
AuthorsWithers-Martinez, C. / Cambillau, C.
Citation
Journal: Structure / Year: 1996
Title: A pancreatic lipase with a phospholipase A1 activity: crystal structure of a chimeric pancreatic lipase-related protein 2 from guinea pig.
Authors: Withers-Martinez, C. / Carriere, F. / Verger, R. / Bourgeois, D. / Cambillau, C.
#1: Journal: Biochemistry / Year: 1994
Title: Evidence for a Pancreatic Lipase Subfamily with New Kinetic Properties
Authors: Thirstrup, K. / Verger, R. / Carriere, F.
#2: Journal: Protein Eng. / Year: 1994
Title: Structure-Function Relationships in Naturally Occurring Mutants of Pancreatic Lipase
Authors: Carriere, F. / Thirstrup, K. / Boel, E. / Verger, R. / Thim, L.
#3: Journal: Biochemistry / Year: 1993
Title: A Structural Domain (the Lid) Found in Pancreatic Lipases is Absent in the Guinea Pig (Phospho)Lipase
Authors: Hjorth, A. / Carriere, F. / Cudrey, C. / Woldike, H. / Boel, E. / Lawson, D.M. / Ferrato, F. / Cambillau, C. / Dodson, G.G. / Thim, L. / al., et
History
DepositionJul 13, 1996Processing site: BNL
Revision 1.0Feb 12, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 4, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_entry_details.has_protein_modification / _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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: RP2 LIPASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9162
Polymers47,8761
Non-polymers401
Water4,450247
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.000, 55.900, 144.000
Angle α, β, γ (deg.)90.00, 93.20, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein RP2 LIPASE / RELATED PROTEIN 2 LIPASE


Mass: 47875.840 Da / Num. of mol.: 1
Mutation: DOMAIN EXCHANGE (C-TERMINUS, RESIDUES 336 - 449) WITH HUMAN PANCREATIC LIPASE
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cavia porcellus (domestic guinea pig) / Cell line: SF9 / Organ: PANCREATIC / Plasmid: PVL1393 / Production host: SF9 CELLS / Strain (production host): SF9
References: UniProt: P16233, UniProt: P81139*PLUS, triacylglycerol lipase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 247 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE C-TERMINAL DOMAIN OF GPLRP2 (336 - 449) HAS BEEN REPLACED BY THE C-TERMINAL DOMAIN OF HPL BY ...THE C-TERMINAL DOMAIN OF GPLRP2 (336 - 449) HAS BEEN REPLACED BY THE C-TERMINAL DOMAIN OF HPL BY MUTAGENESIS EXPERIMENTS.
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 53 %
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 6.5 / Method: vapor diffusion, hanging drop / Details: used to seeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
111 mg/mlprotein1drop
250 mM1dropNaCl
310 mMMES1drop
4100 mMbicine1reservoir
51 M1reservoirLiCl
610-15 %(w/v)PEG60001reservoir

-
Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: MAR scanner 180 mm plate / Detector: IMAGE PLATE
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 27079 / % possible obs: 92.6 % / Observed criterion σ(I): 1 / Redundancy: 3.5 % / Rmerge(I) obs: 0.113
Reflection
*PLUS
Highest resolution: 2.1 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.099
Reflection shell
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 2.15 Å / % possible obs: 88.9 %

-
Processing

Software
NameClassification
DENZOdata reduction
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.01→6 Å / σ(F): 2
Details: REGION 207 - 214 IS DISORDERED AND MODELLED STEREOCHEMICALLY, BASED ON HUMAN PANCREATIC LIPASE (HPL) STRUCTURE. OCCUPATION OF THESE RESIDUES HAS BEEN SET TO 0.0. THE SHORT LOOP CONTAINED ...Details: REGION 207 - 214 IS DISORDERED AND MODELLED STEREOCHEMICALLY, BASED ON HUMAN PANCREATIC LIPASE (HPL) STRUCTURE. OCCUPATION OF THESE RESIDUES HAS BEEN SET TO 0.0. THE SHORT LOOP CONTAINED BETWEEN THE TWO SIDES OF THE DISULFIDE BRIDGE (CYS 4 - CYS 10) PRESENTS IN THE TURN A SER CLOSE TO THE EPSILON CONFORMATION.
RfactorNum. reflection
Rfree0.246 -
Rwork0.188 -
obs0.188 23574
Refinement stepCycle: LAST / Resolution: 2.01→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4121 0 1 245 4367
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
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_deg1.67
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
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
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.1 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more