[English] 日本語
Yorodumi
- PDB-4zwn: Crystal Structure of a Soluble Variant of the Monoglyceride Lipas... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4zwn
TitleCrystal Structure of a Soluble Variant of the Monoglyceride Lipase from Saccharomyces Cerevisiae
ComponentsMonoglyceride lipase
KeywordsHYDROLASE / Monoglyceride Lipase / Monoacylglycerol Lipase / Serine Hydrolase / Alpha/Beta Hydrolase
Function / homology
Function and homology information


Acyl chain remodeling of DAG and TAG / Arachidonate production from DAG / acylglycerol lipase / triglyceride catabolic process / monoacylglycerol lipase activity / serine hydrolase activity / triglyceride metabolic process / lipid droplet / cell periphery / mitochondrial outer membrane ...Acyl chain remodeling of DAG and TAG / Arachidonate production from DAG / acylglycerol lipase / triglyceride catabolic process / monoacylglycerol lipase activity / serine hydrolase activity / triglyceride metabolic process / lipid droplet / cell periphery / mitochondrial outer membrane / endoplasmic reticulum / mitochondrion / membrane / plasma membrane / cytoplasm
Similarity search - Function
: / Serine aminopeptidase, S33 / Serine aminopeptidase, S33 / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NITRATE ION / Monoglyceride lipase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.491 Å
AuthorsAschauer, P. / Rengachari, S. / Gruber, K. / Oberer, M.
Funding support Austria, 2items
OrganizationGrant numberCountry
Austrian Science FundP24857 Austria
DK Molecular EnzymologyW901-B12 Austria
CitationJournal: Biochim.Biophys.Acta / Year: 2016
Title: Crystal structure of the Saccharomyces cerevisiae monoglyceride lipase Yju3p.
Authors: Aschauer, P. / Rengachari, S. / Lichtenegger, J. / Schittmayer, M. / Das, K.M. / Mayer, N. / Breinbauer, R. / Birner-Gruenberger, R. / Gruber, C.C. / Zimmermann, R. / Gruber, K. / Oberer, M.
History
DepositionMay 19, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 27, 2016Provider: repository / Type: Initial release
Revision 1.1May 25, 2016Group: Database references
Revision 1.2Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Monoglyceride lipase
B: Monoglyceride lipase
C: Monoglyceride lipase
D: Monoglyceride lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,4378
Polymers152,1604
Non-polymers2774
Water7,350408
1
A: Monoglyceride lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1022
Polymers38,0401
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Monoglyceride lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1362
Polymers38,0401
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Monoglyceride lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1362
Polymers38,0401
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Monoglyceride lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0632
Polymers38,0401
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)77.196, 108.566, 167.667
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
Monoglyceride lipase / MGL / Monoacylglycerol hydrolase / MGH / Monoacylglycerol lipase / MAGL / Serine hydrolase YJU3


Mass: 38040.082 Da / Num. of mol.: 4 / Fragment: UNP residues 2-313 / Mutation: Q264R, L175S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: YJU3, YKL094W, YKL441 / Plasmid: pPRoEx Htb / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P28321, acylglycerol lipase
#2: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 408 / 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: 2.48 Å3/Da / Density % sol: 50.5 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8.7
Details: 0.1 M Bicine/Trizma base pH 8.7, 10% w/v PEG 20 000, 20% v/v PEG MME 550 and 0.03 M sodium nitrate, 0.03 M disodium hydrogen phosphate, 0.03 M ammonium sulphate. Microseeding

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9999 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 20, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 2.49→45.27 Å / Num. obs: 49134 / % possible obs: 98.4 % / Redundancy: 8.9 % / Biso Wilson estimate: 39.25 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.198 / Rpim(I) all: 0.07 / Net I/σ(I): 10.5 / Num. measured all: 439569 / Scaling rejects: 10
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.49-2.578.51.4981.73535541470.490.53691.6
9.96-45.2780.06130.865198130.9960.02294.6

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
Aimless0.1.29data scaling
PDB_EXTRACT3.15data extraction
Auto-Rickshawphasing
RefinementMethod to determine structure: MAD / Resolution: 2.491→45.27 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.28 / Stereochemistry target values: ML
Details: The authors performed MAD experiment with Potassium tetra nitro Platinate as heavy atom complex using the wavelengths 1.07155(peak), 1.07182(inflection) and 1.06878(remote). The data was ...Details: The authors performed MAD experiment with Potassium tetra nitro Platinate as heavy atom complex using the wavelengths 1.07155(peak), 1.07182(inflection) and 1.06878(remote). The data was uploaded to the autorickshaw server (http://www.embl-hamburg.de/Auto-Rickshaw/) and then used the biggest fragment with the best e-density fit of the resulting model to do Molecular replacement into a nativ data set with higher resolution. After this, the model building process was done manually using phenix.autobuild. The data in the session are for the native data set. So the phasing method was a mixture of MR and MAD.
RfactorNum. reflection% reflection
Rfree0.224 2498 5.09 %
Rwork0.1883 --
obs0.1901 49067 98.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.491→45.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9909 0 15 408 10332
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00510192
X-RAY DIFFRACTIONf_angle_d0.77113758
X-RAY DIFFRACTIONf_dihedral_angle_d12.9583781
X-RAY DIFFRACTIONf_chiral_restr0.041415
X-RAY DIFFRACTIONf_plane_restr0.0031792
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4915-2.53940.33691310.27822229X-RAY DIFFRACTION87
2.5394-2.59120.32311290.2612587X-RAY DIFFRACTION98
2.5912-2.64750.31151490.25332564X-RAY DIFFRACTION99
2.6475-2.70910.26821390.24312557X-RAY DIFFRACTION99
2.7091-2.77690.31781310.24952589X-RAY DIFFRACTION99
2.7769-2.85190.26371520.24122571X-RAY DIFFRACTION99
2.8519-2.93580.28731390.23752562X-RAY DIFFRACTION99
2.9358-3.03060.30971300.23622591X-RAY DIFFRACTION99
3.0306-3.13890.23891310.21862584X-RAY DIFFRACTION99
3.1389-3.26450.27981370.21392604X-RAY DIFFRACTION99
3.2645-3.4130.2481340.20662613X-RAY DIFFRACTION99
3.413-3.59290.23641340.19792609X-RAY DIFFRACTION99
3.5929-3.81790.20061390.18262636X-RAY DIFFRACTION99
3.8179-4.11250.18361570.16442591X-RAY DIFFRACTION99
4.1125-4.5260.18011300.14372661X-RAY DIFFRACTION99
4.526-5.18010.17861560.14092627X-RAY DIFFRACTION99
5.1801-6.52330.17821440.15842687X-RAY DIFFRACTION99
6.5233-45.27760.17451360.14872707X-RAY DIFFRACTION95

+
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