[English] 日本語
Yorodumi
- PDB-1akn: STRUCTURE OF BILE-SALT ACTIVATED LIPASE -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 1akn
TitleSTRUCTURE OF BILE-SALT ACTIVATED LIPASE
ComponentsBILE-SALT ACTIVATED LIPASE
KeywordsHYDROLASE / SERINE ESTERASE / LIPID DEGRADATION / GLYCOPROTEIN / CARBOXYLIC ESTERASE / HYDROLASE()
Function / homologyalpha/beta hydrolase fold / Carboxylesterase type B, active site / Carboxylesterases type-B signature 2. / Carboxylesterases type-B serine active site. / Carboxylesterase family / Bile salt-activated lipase / Alpha/Beta hydrolase fold / Carboxylesterase type B, conserved site / Carboxylesterase, type B / sterol esterase ...alpha/beta hydrolase fold / Carboxylesterase type B, active site / Carboxylesterases type-B signature 2. / Carboxylesterases type-B serine active site. / Carboxylesterase family / Bile salt-activated lipase / Alpha/Beta hydrolase fold / Carboxylesterase type B, conserved site / Carboxylesterase, type B / sterol esterase / sterol esterase activity / triacylglycerol lipase / triglyceride lipase activity / carboxylic ester hydrolase activity / lipid catabolic process / extracellular region / cytoplasm / Bile salt-activated lipase
Function and homology information
Specimen sourceBos taurus (cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / 2.8 Å resolution
AuthorsWang, X. / Zhang, X.
CitationJournal: Structure / Year: 1997
Title: The crystal structure of bovine bile salt activated lipase: insights into the bile salt activation mechanism.
Authors: Wang, X. / Wang, C.S. / Tang, J. / Dyda, F. / Zhang, X.C.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: May 23, 1997 / Release: May 27, 1998
RevisionDateData content typeGroupProviderType
1.0May 27, 1998Structure modelrepositoryInitial release
1.1Mar 24, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelNon-polymer description / Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: BILE-SALT ACTIVATED LIPASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,8332
Polyers63,6111
Non-polymers2211
Water0
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)94.390, 94.390, 144.510
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP 31 2 1

-
Components

#1: Protein/peptide BILE-SALT ACTIVATED LIPASE / CARBOXYL ESTER LIPASE / STEROL ESTERASE / CHOLESTEROL ESTERASE / PANCREATIC LYSOPHOSPHOLIPASE


Mass: 63611.363 Da / Num. of mol.: 1 / Source: (natural) Bos taurus (cattle) / Genus: Bos / Organ: PANCREAS / References: UniProt: P30122, triacylglycerol lipase
#2: Chemical ChemComp-NAG / N-ACETYL-D-GLUCOSAMINE


Mass: 221.208 Da / Num. of mol.: 1 / Formula: C8H15NO6 / N-Acetylglucosamine

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.93 / Density percent sol: 58 %
Crystal growpH: 7 / Details: pH 7.
Crystal grow
*PLUS
Temp: 20 ℃ / Method: vapor diffusion, hanging drop
components of the solutions
*PLUS
IDConcCommon nameCrystal IDSol ID
112.5 mg/mlprotein1drop
20.9 Mammonium sulfate1drop
32.5 %isopropanol1drop
40.5 mMzwittergent 3-121drop
51.8 Mammonium sulfate1reservoir
65 %isopropanol1reservoir
71 mMzwittergent 3-121reservoir

-
Data collection

DiffractionMean temperature: 288 kelvins
SourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Details: MIRROR / Detector: IMAGE PLATE / Collection date: Dec 1, 1996
RadiationMonochromator: NI FILTER / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionB iso Wilson estimate: 66.1 Å2 / D resolution high: 2.8 Å / D resolution low: 33.7 Å / Number obs: 18614 / Observed criterion sigma I: 0 / Rmerge I obs: 0.066 / NetI over sigmaI: 13.8 / Redundancy: 2.53 % / Percent possible obs: 98.4
Reflection shellRmerge I obs: 0.39 / Highest resolution: 2.8 Å / Lowest resolution: 2.9 Å / MeanI over sigI obs: 2.8 / Redundancy: 1.3 % / Percent possible all: 91.2
Reflection
*PLUS
D resolution low: 34 Å
Reflection shell
*PLUS
Percent possible obs: 99.8 / Rmerge I obs: 0.391

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
RefineMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ACE
Details: AT FINAL STEP, ALL DATA IN 8 - 2.8 A WERE USED TO CARRY OUT A RESTRAINED TEMPERATURE FACTOR REFINEMENT BY TNT.
R Free selection details: RANDOM
Displacement parametersB iso mean: 47.6 Å2
Least-squares processR factor R free: 0.29 / R factor R work: 0.211 / R factor obs: 0.211 / Highest resolution: 2.8 Å / Lowest resolution: 8 Å / Number reflection R free: 1706 / Number reflection obs: 17178 / Percent reflection R free: 9.3 / Percent reflection obs: 95.3
Refine hist #LASTHighest resolution: 2.8 Å / Lowest resolution: 8 Å
Number of atoms included #LASTProtein: 4261 / Nucleic acid: 0 / Ligand: 14 / Solvent: 0 / Total: 4275
Refine LS restraints
Refine IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
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_deg1.5
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.8
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.32
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
Xplor file
Refine IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2NAG.PARNAG.TOP
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Least-squares process
*PLUS
R factor R free: 0.283 / R factor obs: 0.216
Refine LS restraints
*PLUS
Refine IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.8
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.32

+
About Yorodumi

-
News

-
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. See below links for details.
  • 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

-
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

+
Apr 13, 2016. Omokage search got faster

Omokage search got faster

  • The computation time became ~1/2 compared to the previous version by re-optimization of data accession
  • Enjoy "shape similarity" of biomolecules, more!

Related info.: Omokage search

Read more

-
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.

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