[English] 日本語
Yorodumi
- PDB-6cl4: LipC12 - Lipase from metagenomics -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6cl4
TitleLipC12 - Lipase from metagenomics
ComponentsLipase C12
KeywordsHYDROLASE / Lipase
Function / homology
Function and homology information


triacylglycerol lipase / triacylglycerol lipase activity
Similarity search - Function
alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesuncultured bacterium (environmental samples)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.64 Å
AuthorsIulek, J. / Martini, V.P. / Krieger, N. / Glogauer, A. / Souza, E.M.
CitationJournal: N Biotechnol / Year: 2019
Title: Structure solution and analyses of the first true lipase obtained from metagenomics indicate potential for increased thermostability.
Authors: Martini, V.P. / Krieger, N. / Glogauer, A. / Souza, E.M. / Iulek, J.
History
DepositionMar 1, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2019Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Lipase C12


Theoretical massNumber of molelcules
Total (without water)33,4341
Polymers33,4341
Non-polymers00
Water2,702150
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.500, 58.500, 192.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122

-
Components

#1: Protein Lipase C12


Mass: 33433.777 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) uncultured bacterium (environmental samples)
Gene: lipc12 / Production host: Escherichia coli (E. coli) / References: UniProt: G1APT8, triacylglycerol lipase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / 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: 50.4 % / Description: needles
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 2.0 M sodium formate and 0.1 M bis-tris propane, pH 7.0 using a protein concentration of 10 mg / mL. Crystals grown for ten weeks

-
Data collection

DiffractionMean temperature: 100 K / Ambient temp details: nitrogen stream
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 29, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.64→58.5 Å / Num. obs: 10489 / % possible obs: 95.5 % / Observed criterion σ(I): -3 / Redundancy: 8.82 % / Rrim(I) all: 0.14 / Net I/σ(I): 18.91
Reflection shellResolution: 2.64→2.72 Å / Redundancy: 8.38 % / Mean I/σ(I) obs: 4.29 / Num. unique obs: 851 / Rrim(I) all: 0.641 / % possible all: 97.7

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSVERSION December 28, 2009data reduction
XSCALEVERSION January 30, 2009data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EX9

1ex9


Resolution: 2.64→48.175 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.63
RfactorNum. reflection% reflection
Rfree0.251 503 4.8 %
Rwork0.1922 --
obs0.195 10487 99.42 %
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.3 Å
Refinement stepCycle: LAST / Resolution: 2.64→48.175 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2181 0 0 150 2331
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022250
X-RAY DIFFRACTIONf_angle_d0.4473058
X-RAY DIFFRACTIONf_dihedral_angle_d9.172807
X-RAY DIFFRACTIONf_chiral_restr0.018345
X-RAY DIFFRACTIONf_plane_restr0.002400
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.64-2.90570.2831120.242423X-RAY DIFFRACTION99
2.9057-3.3260.27571440.2162419X-RAY DIFFRACTION100
3.326-4.19010.23061200.17612504X-RAY DIFFRACTION100
4.1901-48.1830.23741270.17572638X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 4.5125 Å / Origin y: 21.2 Å / Origin z: 22.0314 Å
111213212223313233
T0.1718 Å20.0669 Å20.0072 Å2-0.2189 Å20.0056 Å2--0.1874 Å2
L0.7649 °20.6386 °20.9212 °2-1.2731 °21.0468 °2--3.0022 °2
S0.0214 Å °-0.0749 Å °-0.0352 Å °-0.0523 Å °-0.001 Å °-0.0416 Å °-0.0453 Å °-0.0924 Å °-0.0238 Å °
Refinement TLS groupSelection details: chain A

+
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