[English] 日本語
Yorodumi
- PDB-1ein: THE STRUCTURAL ORIGINS OF INTERFACIAL ACTIVATION IN THERMOMYCES (... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ein
TitleTHE STRUCTURAL ORIGINS OF INTERFACIAL ACTIVATION IN THERMOMYCES (HUMICOLA) LANUGINOSA LIPASE
ComponentsLIPASE
KeywordsHYDROLASE / alpha-beta structure
Function / homology
Function and homology information


triacylglycerol lipase / triglyceride 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
DIUNDECYL PHOSPHATIDYL CHOLINE / Lipase
Similarity search - Component
Biological speciesThermomyces lanuginosus (fungus)
MethodX-RAY DIFFRACTION / Resolution: 3 Å
AuthorsBrozozowski, A.M. / Savage, H.
CitationJournal: Biochemistry / Year: 2000
Title: Structural origins of the interfacial activation in Thermomyces (Humicola) lanuginosa lipase.
Authors: Brzozowski, A.M. / Savage, H. / Verma, C.S. / Turkenburg, J.P. / Lawson, D.M. / Svendsen, A. / Patkar, S.
History
DepositionFeb 26, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 20, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: LIPASE
B: LIPASE
C: LIPASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,8966
Polymers88,0273
Non-polymers1,8693
Water3,315184
1
A: LIPASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9652
Polymers29,3421
Non-polymers6231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: LIPASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9652
Polymers29,3421
Non-polymers6231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: LIPASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9652
Polymers29,3421
Non-polymers6231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)135.950, 135.950, 149.990
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65
DetailsThe biological assembly is a monomer

-
Components

#1: Protein LIPASE /


Mass: 29342.484 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Thermomyces lanuginosus (fungus) / References: UniProt: O59952, triacylglycerol lipase
#2: Chemical ChemComp-PLC / DIUNDECYL PHOSPHATIDYL CHOLINE


Mass: 622.834 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C32H65NO8P / Comment: phospholipid*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 184 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.54 Å3/Da / Density % sol: 72.93 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 8.1
Details: PEG 5000, magnesium chloride, c8e5 , pH 8.1, VAPOR DIFFUSION, HANGING DROP, temperature 110K
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15 mg/mlprotein1drop
210 mMTris-HCl1drop
30.1 MTris-HCl1reservoir
425 mM1reservoirMgCl2
517 %(w/v)mPEG50001reservoir

-
Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Jun 1, 1996
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 3→27.4 Å / Num. all: 91965 / Num. obs: 31460 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Rmerge(I) obs: 0.2 / Net I/σ(I): 3
Reflection shellResolution: 3→3.16 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.139 / Num. unique all: 31460 / % possible all: 100
Reflection
*PLUS
% possible obs: 99.5 %
Reflection shell
*PLUS
% possible obs: 98.2 % / Redundancy: 2.1 % / Rmerge(I) obs: 0.425 / Mean I/σ(I) obs: 1.8

-
Processing

Software
NameVersionClassification
ROTAVATAdata reduction
AMoREphasing
REFMACrefinement
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
RefinementResolution: 3→27.4 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: R-axis data
RfactorNum. reflection% reflectionSelection details
Rfree0.241 1588 -random
Rwork0.21 ---
all-164254 --
obs-31460 99.8 %-
Refinement stepCycle: LAST / Resolution: 3→27.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6189 0 126 184 6499
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.008
X-RAY DIFFRACTIONo_angle_deg0.029
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 34.1 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_plane_restr0.029

+
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