[English] 日本語
Yorodumi
- PDB-6wq1: Eukaryotic LanCL2 protein -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6wq1
TitleEukaryotic LanCL2 protein
ComponentsLanC-like protein 2
KeywordsBIOSYNTHETIC PROTEIN / lanthipeptide / cyclase / zinc
Function / homology
Function and homology information


positive regulation of abscisic acid-activated signaling pathway / phosphatidylinositol-5-phosphate binding / phosphatidylinositol-3-phosphate binding / phosphatidylinositol-4-phosphate binding / cortical actin cytoskeleton / carbohydrate metabolic process / negative regulation of DNA-templated transcription / GTP binding / nucleoplasm / ATP binding ...positive regulation of abscisic acid-activated signaling pathway / phosphatidylinositol-5-phosphate binding / phosphatidylinositol-3-phosphate binding / phosphatidylinositol-4-phosphate binding / cortical actin cytoskeleton / carbohydrate metabolic process / negative regulation of DNA-templated transcription / GTP binding / nucleoplasm / ATP binding / nucleus / plasma membrane / cytosol
Similarity search - Function
LanC-like protein, eukaryotic / Lanthionine synthetase C-like protein / Lanthionine synthetase C-like / Lanthionine synthetase C-like protein / Six-hairpin glycosidase-like superfamily
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.295 Å
AuthorsNair, S.K. / Garg, N.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Cell / Year: 2021
Title: LanCLs add glutathione to dehydroamino acids generated at phosphorylated sites in the proteome.
Authors: Lai, K.Y. / Galan, S.R.G. / Zeng, Y. / Zhou, T.H. / He, C. / Raj, R. / Riedl, J. / Liu, S. / Chooi, K.P. / Garg, N. / Zeng, M. / Jones, L.H. / Hutchings, G.J. / Mohammed, S. / Nair, S.K. / ...Authors: Lai, K.Y. / Galan, S.R.G. / Zeng, Y. / Zhou, T.H. / He, C. / Raj, R. / Riedl, J. / Liu, S. / Chooi, K.P. / Garg, N. / Zeng, M. / Jones, L.H. / Hutchings, G.J. / Mohammed, S. / Nair, S.K. / Chen, J. / Davis, B.G. / van der Donk, W.A.
History
DepositionApr 28, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 5, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 17, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: LanC-like protein 2
B: LanC-like protein 2
C: LanC-like protein 2
D: LanC-like protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)203,9558
Polymers203,6934
Non-polymers2624
Water13,367742
1
A: LanC-like protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,9892
Polymers50,9231
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: LanC-like protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,9892
Polymers50,9231
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: LanC-like protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,9892
Polymers50,9231
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: LanC-like protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,9892
Polymers50,9231
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.415, 108.012, 152.013
Angle α, β, γ (deg.)90.000, 91.260, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
LanC-like protein 2 / lanCL2 / Testis-specific adriamycin sensitivity protein


Mass: 50923.273 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LANCL2, GPR69B, TASP / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NS86
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 742 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.11 Å3/Da / Density % sol: 41.76 %
Crystal growTemperature: 273 K / Method: vapor diffusion, hanging drop / Details: PEG400, PEG4000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 18, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.295→50 Å / Num. obs: 71159 / % possible obs: 94 % / Redundancy: 5.6 % / CC1/2: 0.882 / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.046 / Net I/σ(I): 13.9
Reflection shellResolution: 2.295→2.34 Å / Rmerge(I) obs: 0.283 / Num. unique obs: 2209 / Rpim(I) all: 0.166

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3E6U

3e6u


Resolution: 2.295→37.608 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.98
RfactorNum. reflection% reflection
Rfree0.2447 3559 5.01 %
Rwork0.1837 --
obs0.1868 71039 93.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 76.7 Å2 / Biso mean: 23.8287 Å2 / Biso min: 6.13 Å2
Refinement stepCycle: final / Resolution: 2.295→37.608 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12729 0 4 742 13475
Biso mean--20.21 27.49 -
Num. residues----1583
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00813033
X-RAY DIFFRACTIONf_angle_d0.90417610
X-RAY DIFFRACTIONf_dihedral_angle_d3.3847780
X-RAY DIFFRACTIONf_chiral_restr0.0491879
X-RAY DIFFRACTIONf_plane_restr0.0052250
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.295-2.32640.3345980.225157556
2.3264-2.35960.26331010.2128200869
2.3596-2.39480.2931070.1987217575
2.3948-2.43220.26761230.1972224881
2.4322-2.47210.27161440.1909245786
2.4721-2.51470.25541310.1934261790
2.5147-2.56040.30961130.1989270794
2.5604-2.60970.26251400.2036278096
2.6097-2.66290.2531580.2051278999
2.6629-2.72080.27731600.20572861100
2.7208-2.78410.28661530.22885100
2.7841-2.85370.2621300.20252858100
2.8537-2.93080.29551550.20392892100
2.9308-3.0170.27821550.20522838100
3.017-3.11440.26681490.19322893100
3.1144-3.22560.261420.19192885100
3.2256-3.35470.27761710.1872844100
3.3547-3.50720.24961540.17362900100
3.5072-3.6920.21161360.16882869100
3.692-3.92310.21011620.15572858100
3.9231-4.22560.20971550.15592890100
4.2256-4.65020.18141560.15152896100
4.6502-5.32140.21951480.16742904100
5.3214-6.69830.24571670.20512906100
6.6983-37.6080.20621510.17932945100

+
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