[English] 日本語
Yorodumi
- PDB-5v12: Crystal structure of Carbon Sulfoxide lyase, Egt2 Y134F with sulf... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5v12
TitleCrystal structure of Carbon Sulfoxide lyase, Egt2 Y134F with sulfenic acid intermediate
Components(Hercynylcysteine sulfoxide lyase) x 2
KeywordsLYASE / C-S lyase / PLP dependent
Function / homology
Function and homology information


hercynylcysteine sulfoxide lyase activity (ergothioneine-forming) / Lyases; Carbon-sulfur lyases / nucleus / cytoplasm
Similarity search - Function
Aminotransferase class V domain / Aminotransferase class-V / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
Chem-8QJ / FORMIC ACID / Hercynylcysteine sulfoxide lyase
Similarity search - Component
Biological speciesNeurospora crassa OR74A (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.451 Å
AuthorsIrani, S. / Zhang, Y.
CitationJournal: Cell Chem Biol / Year: 2018
Title: Snapshots of C-S Cleavage in Egt2 Reveals Substrate Specificity and Reaction Mechanism.
Authors: Irani, S. / Naowarojna, N. / Tang, Y. / Kathuria, K.R. / Wang, S. / Dhembi, A. / Lee, N. / Yan, W. / Lyu, H. / Costello, C.E. / Liu, P. / Zhang, Y.J.
History
DepositionMar 1, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 7, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2019Group: Data collection / Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / entity / entity_name_com / struct
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 / _entity.pdbx_description / _entity_name_com.name / _struct.title
Revision 2.0Oct 4, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Polymer sequence / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / entity_name_com / entity_poly / entity_src_gen / pdbx_initial_refinement_model / pdbx_validate_main_chain_plane / struct_conf
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _entity_name_com.name / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.pdbx_gene_src_scientific_name
Revision 2.1Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 2.2Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
E: Hercynylcysteine sulfoxide lyase
G: Hercynylcysteine sulfoxide lyase
F: Hercynylcysteine sulfoxide lyase
H: Hercynylcysteine sulfoxide lyase
C: Hercynylcysteine sulfoxide lyase
D: Hercynylcysteine sulfoxide lyase
A: Hercynylcysteine sulfoxide lyase
B: Hercynylcysteine sulfoxide lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)452,35818
Polymers451,4978
Non-polymers86110
Water7,422412
1
E: Hercynylcysteine sulfoxide lyase
F: Hercynylcysteine sulfoxide lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,1915
Polymers112,8532
Non-polymers3383
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6370 Å2
ΔGint-23 kcal/mol
Surface area32190 Å2
MethodPISA
2
G: Hercynylcysteine sulfoxide lyase
H: Hercynylcysteine sulfoxide lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,9454
Polymers112,8532
Non-polymers922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6600 Å2
ΔGint-20 kcal/mol
Surface area32120 Å2
MethodPISA
3
C: Hercynylcysteine sulfoxide lyase
D: Hercynylcysteine sulfoxide lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,0324
Polymers112,9402
Non-polymers922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6420 Å2
ΔGint-22 kcal/mol
Surface area31990 Å2
MethodPISA
4
A: Hercynylcysteine sulfoxide lyase
B: Hercynylcysteine sulfoxide lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,1915
Polymers112,8532
Non-polymers3383
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6800 Å2
ΔGint-20 kcal/mol
Surface area32190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.021, 195.158, 110.100
Angle α, β, γ (deg.)90.00, 91.47, 90.00
Int Tables number4
Space group name H-MP1211
DetailsDimer as determined by gel filtration

-
Components

#1: Protein
Hercynylcysteine sulfoxide lyase / Ergothioneine biosynthesis protein 2 / PLP-binding cysteine desulfurase / PLP-dependent C-S lyase


Mass: 56426.262 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neurospora crassa OR74A (fungus)
Strain: ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987
Gene: egt-2, NCU11365 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A7UX13, Lyases; Carbon-sulfur lyases
#2: Protein Hercynylcysteine sulfoxide lyase / Ergothioneine biosynthesis protein 2 / PLP-binding cysteine desulfurase / PLP-dependent C-S lyase


Mass: 56513.340 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neurospora crassa OR74A (fungus)
Strain: ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987
Gene: egt-2, NCU11365 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A7UX13, Lyases; Carbon-sulfur lyases
#3: Chemical
ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical ChemComp-8QJ / (2~{S})-3-(2-oxidanylsulfanyl-1~{H}-imidazol-4-yl)-2-(trimethyl-$l^{4}-azanyl)propanoic acid


Mass: 246.307 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H16N3O3S
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 412 / 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: 2.82 Å3/Da / Density % sol: 56.33 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 30% PEG 3350, 50mM HEPES pH 7.5, 200mM sodium formate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.45→50 Å / Num. obs: 146021 / % possible obs: 91.2 % / Redundancy: 2.9 % / Net I/σ(I): 8.46

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5UTS

5uts


Resolution: 2.451→49.577 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.33
RfactorNum. reflection% reflection
Rfree0.2717 1988 1.36 %
Rwork0.222 --
obs0.2227 146021 91.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.451→49.577 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms27896 0 56 412 28364
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00428577
X-RAY DIFFRACTIONf_angle_d0.60738716
X-RAY DIFFRACTIONf_dihedral_angle_d16.54817180
X-RAY DIFFRACTIONf_chiral_restr0.0444278
X-RAY DIFFRACTIONf_plane_restr0.0044990
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4509-2.51220.37531320.32499147X-RAY DIFFRACTION81
2.5122-2.58010.31881110.31169616X-RAY DIFFRACTION85
2.5801-2.6560.37251630.29529927X-RAY DIFFRACTION89
2.656-2.74170.3431600.295310370X-RAY DIFFRACTION92
2.7417-2.83970.33431240.274510546X-RAY DIFFRACTION94
2.8397-2.95340.37551390.269910689X-RAY DIFFRACTION95
2.9534-3.08780.30721470.266210574X-RAY DIFFRACTION94
3.0878-3.25050.27611550.246610674X-RAY DIFFRACTION94
3.2505-3.45410.30331370.23510560X-RAY DIFFRACTION94
3.4541-3.72080.29071440.214810531X-RAY DIFFRACTION93
3.7208-4.0950.24071490.187110446X-RAY DIFFRACTION93
4.095-4.68720.2131430.170810431X-RAY DIFFRACTION92
4.6872-5.90380.23281380.179510334X-RAY DIFFRACTION91
5.9038-49.5870.19591460.180610188X-RAY DIFFRACTION89

+
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