[English] 日本語
Yorodumi
- PDB-5mal: Crystal structure of extracelular lipase from Streptomyces rimosu... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5mal
TitleCrystal structure of extracelular lipase from Streptomyces rimosus at 1.7A resolution
ComponentsLipase
KeywordsHYDROLASE / SGNH hydrolase / multifunctional enzyme from Streptomyces rimosus / quantum-mechanical study / catalytic mechanism / catalytic dyad - Ser /His
Function / homology
Function and homology information


: / : / palmitoyl-CoA hydrolase / phospholipase activity / Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases / triacylglycerol lipase / carboxylic ester hydrolase activity / triglyceride lipase activity / lipid catabolic process / extracellular region
Similarity search - Function
Streptomyces scabies esterase-like / SGNH hydrolase / SGNH hydrolase-type esterase domain / GDSL-like Lipase/Acylhydrolase family / SGNH hydrolase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesStreptomyces rimosus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.708 Å
AuthorsStefanic, Z.
CitationJournal: ACS Chem. Biol. / Year: 2017
Title: Catalytic Dyad in the SGNH Hydrolase Superfamily: In-depth Insight into Structural Parameters Tuning the Catalytic Process of Extracellular Lipase from Streptomyces rimosus.
Authors: Lescic Asler, I. / Stefanic, Z. / Marsavelski, A. / Vianello, R. / Kojic-Prodic, B.
History
DepositionNov 3, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 14, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 28, 2017Group: Database references / Category: citation / Item: _citation.country / _citation.title
Revision 1.2Aug 2, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_volume ..._citation.country / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 17, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Lipase
B: Lipase


Theoretical massNumber of molelcules
Total (without water)48,3872
Polymers48,3872
Non-polymers00
Water9,044502
1
A: Lipase


Theoretical massNumber of molelcules
Total (without water)24,1941
Polymers24,1941
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lipase


Theoretical massNumber of molelcules
Total (without water)24,1941
Polymers24,1941
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.090, 78.690, 56.560
Angle α, β, γ (deg.)90.000, 104.490, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Lipase / Diheptanoyl glycerophosphocholine esterase / Extracellular lipase / GDSL-like lipase / Palmitoyl- ...Diheptanoyl glycerophosphocholine esterase / Extracellular lipase / GDSL-like lipase / Palmitoyl-CoA hydrolase / SRL


Mass: 24193.740 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Streptomyces rimosus (bacteria)
References: UniProt: Q93MW7, triacylglycerol lipase, Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases, palmitoyl-CoA hydrolase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 502 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1M MES, 25 % PEG 2000 MME

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 0.999 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Sep 18, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999 Å / Relative weight: 1
ReflectionResolution: 1.708→24.007 Å / Num. all: 34875 / Num. obs: 34875 / % possible obs: 99.5 % / Redundancy: 3.8 % / Biso Wilson estimate: 14.67 Å2 / Rpim(I) all: 0.055 / Rrim(I) all: 0.108 / Rsym value: 0.093 / Net I/av σ(I): 4.492 / Net I/σ(I): 9.3 / Num. measured all: 131164
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.71-1.83.20.3262.1196.5
1.8-1.913.80.23131100
1.91-2.043.90.1634.31100
2.04-2.213.90.12851100
2.21-2.423.90.10361100
2.42-2.73.90.0916.71100
2.7-3.123.90.0787.11100
3.12-3.823.90.0737.21100
3.82-5.43.90.0786.31100
5.4-24.0073.70.0597.1198.8

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.71 Å24.01 Å
Translation1.71 Å24.01 Å

-
Processing

Software
NameVersionClassification
PHENIXrefinement
SCALA3.3.9data scaling
PHASER2.5.3phasing
PDB_EXTRACT3.22data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4hyq

4hyq


Resolution: 1.708→24.007 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.08
RfactorNum. reflection% reflection
Rfree0.2142 1999 5.74 %
Rwork0.1647 --
obs0.1676 34832 99.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 50.04 Å2 / Biso mean: 17.122 Å2 / Biso min: 4.5 Å2
Refinement stepCycle: final / Resolution: 1.708→24.007 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3400 0 0 502 3902
Biso mean---24.51 -
Num. residues----468
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073497
X-RAY DIFFRACTIONf_angle_d1.2374762
X-RAY DIFFRACTIONf_chiral_restr0.046542
X-RAY DIFFRACTIONf_plane_restr0.005630
X-RAY DIFFRACTIONf_dihedral_angle_d13.631206
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7081-1.75080.29481310.25282164229593
1.7508-1.79810.29631450.216523632508100
1.7981-1.8510.2951420.196823262468100
1.851-1.91070.25571430.200823602503100
1.9107-1.9790.22591430.187423432486100
1.979-2.05810.25821430.176523502493100
2.0581-2.15180.21381430.169523532496100
2.1518-2.26510.22041430.177623462489100
2.2651-2.40690.22181440.163723502494100
2.4069-2.59260.26631440.172923742518100
2.5926-2.85310.2271440.168823692513100
2.8531-3.2650.20121430.159923522495100
3.265-4.11030.16021440.131923742518100
4.1103-24.00950.16311470.136324092556100

+
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