[English] 日本語
Yorodumi
- PDB-1tib: CONFORMATIONAL LABILITY OF LIPASES OBSERVED IN THE ABSENCE OF AN ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1tib
TitleCONFORMATIONAL LABILITY OF LIPASES OBSERVED IN THE ABSENCE OF AN OIL-WATER INTERFACE: CRYSTALLOGRAPHIC STUDIES OF ENZYMES FROM THE FUNGI HUMICOLA LANUGINOSA AND RHIZOPUS DELEMAR
ComponentsLIPASE
KeywordsHYDROLASE(CARBOXYLIC ESTERASE)
Function / homology
Function and homology information


triacylglycerol lipase / triacylglycerol lipase activity / lipid catabolic process
Similarity search - Function
Mono-/di-acylglycerol lipase, N-terminal / Lipase 3 N-terminal region / Fungal lipase-like domain / Lipase (class 3) / Lipases, serine active site. / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesThermomyces lanuginosus (fungus)
MethodX-RAY DIFFRACTION / Resolution: 1.84 Å
AuthorsDerewenda, U. / Swenson, L. / Wei, Y. / Derewenda, Z.S.
Citation
Journal: J.Lipid Res. / Year: 1994
Title: Conformational lability of lipases observed in the absence of an oil-water interface: crystallographic studies of enzymes from the fungi Humicola lanuginosa and Rhizopus delemar.
Authors: Derewenda, U. / Swenson, L. / Wei, Y. / Green, R. / Kobos, P.M. / Joerger, R. / Haas, M.J. / Derewenda, Z.S.
#1: Journal: Nat.Struct.Biol. / Year: 1994
Title: An Unusual Buried Polar Cluster in a Family of Fungal Lipases
Authors: Derewenda, U. / Swenson, L. / Green, R. / Wei, Y. / Dodson, G.G. / Yamaguchi, S. / Haas, M.J. / Derewenda, Z.S.
#2: Journal: Protein Eng. / Year: 1994
Title: Current Progress in Crystallographic Studies of New Lipases from Filamentous Fungi
Authors: Derewenda, U. / Swenson, L. / Green, R. / Wei, Y. / Yamaguchi, S. / Joerger, R. / Haas, M.J. / Derewenda, Z.S.
History
DepositionDec 6, 1993Processing site: BNL
Revision 1.0Jan 26, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: LIPASE


Theoretical massNumber of molelcules
Total (without water)29,3421
Polymers29,3421
Non-polymers00
Water6,413356
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)103.165, 51.994, 45.733
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: CIS PROLINE - PRO 207 / 2: CIS PROLINE - PRO 218

-
Components

#1: Protein LIPASE


Mass: 29342.484 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermomyces lanuginosus (fungus) / References: UniProt: O59952, triacylglycerol lipase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 356 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.09 Å3/Da / Density % sol: 41.13 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
11.2 %protein1drop
24 %PEG60001reservoir
3100 mMsodium acetate1reservoir
41 mM1reservoircan be replaced by NaAuCl2K2PdCl4
53 mMspermidine1reservoir

-
Data collection

Reflection
*PLUS
Highest resolution: 1.85 Å / % possible obs: 100 % / Rmerge(I) obs: 0.0472

-
Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 1.84→7.5 Å / σ(F): 0 /
RfactorNum. reflection
obs0.188 19345
Refinement stepCycle: LAST / Resolution: 1.84→7.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2071 0 0 356 2427
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0230.015
X-RAY DIFFRACTIONp_angle_d0.0550.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0530.03
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.1442
X-RAY DIFFRACTIONp_mcangle_it1.8092.5
X-RAY DIFFRACTIONp_scbond_it2.2072.5
X-RAY DIFFRACTIONp_scangle_it3.9874
X-RAY DIFFRACTIONp_plane_restr0.0180.015
X-RAY DIFFRACTIONp_chiral_restr0.1040.06
X-RAY DIFFRACTIONp_singtor_nbd0.1660.15
X-RAY DIFFRACTIONp_multtor_nbd0.2160.15
X-RAY DIFFRACTIONp_xhyhbond_nbd0.2030.15
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor5.0133
X-RAY DIFFRACTIONp_staggered_tor20.65710
X-RAY DIFFRACTIONp_orthonormal_tor32.01915
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Rfactor all: 0.18 / Rfactor obs: 0.167 / Highest resolution: 1.85 Å / Num. reflection obs: 18756 / Rfactor Rwork: 0.167
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.016
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg2.9
X-RAY DIFFRACTIONp_plane_restr0.016

+
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://pdbjlvh1.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