[English] 日本語
Yorodumi
- PDB-8iry: Carbon Sulfoxide lyase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8iry
TitleCarbon Sulfoxide lyase
ComponentsProbable hercynylcysteine sulfoxide lyase
KeywordsLYASE / Carbon Sulfoxide lyase / EgtE
Function / homology
Function and homology information


Lyases; Carbon-sulfur lyases / hercynylcysteine sulfoxide lyase activity (ergothioneine-forming) / ergothioneine biosynthesis from histidine via gamma-glutamyl-hercynylcysteine sulfoxide
Similarity search - Function
Pyridoxal-phosphate-dependent protein EgtE / Aminotransferase class V domain / Aminotransferase class-V / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
PYRIDOXAL-5'-PHOSPHATE / PYRUVIC ACID / Probable hercynylcysteine sulfoxide lyase
Similarity search - Component
Biological speciesMycolicibacterium smegmatis MC2 155 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsGong, W.M. / Wei, L.L. / Liu, L.
Funding support China, Israel, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
Israel Ministry of Science and Technology Israel
CitationJournal: J.Biol.Chem. / Year: 2024
Title: Structure of mycobacterial ergothioneine-biosynthesis C-S lyase EgtE.
Authors: Wei, L. / Liu, L. / Gong, W.
History
DepositionMar 20, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 6, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 / _citation_author.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Probable hercynylcysteine sulfoxide lyase
B: Probable hercynylcysteine sulfoxide lyase
C: Probable hercynylcysteine sulfoxide lyase
D: Probable hercynylcysteine sulfoxide lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,4639
Polymers165,3874
Non-polymers1,0775
Water5,332296
1
A: Probable hercynylcysteine sulfoxide lyase
C: Probable hercynylcysteine sulfoxide lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,2765
Polymers82,6932
Non-polymers5823
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5660 Å2
ΔGint-13 kcal/mol
Surface area27350 Å2
MethodPISA
2
B: Probable hercynylcysteine sulfoxide lyase
D: Probable hercynylcysteine sulfoxide lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,1884
Polymers82,6932
Non-polymers4942
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5280 Å2
ΔGint-18 kcal/mol
Surface area26890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.314, 90.372, 101.531
Angle α, β, γ (deg.)110.77, 105.95, 103.07
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein
Probable hercynylcysteine sulfoxide lyase


Mass: 41346.645 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycolicibacterium smegmatis MC2 155 (bacteria)
Gene: egtE, MSMEG_6246, MSMEI_6085 / Production host: Escherichia coli (E. coli) / References: UniProt: A0R5M7, Lyases; Carbon-sulfur lyases
#2: Chemical
ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H10NO6P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PYR / PYRUVIC ACID


Mass: 88.062 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H4O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 296 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.83 Å3/Da / Density % sol: 67.89 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop
Details: 0.1M HEPES-Na, pH 7.5, 1M NaCl, 0.1M LiSO4, 10% PEG 1000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 23, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.34→50 Å / Num. obs: 95080 / % possible obs: 93.4 % / Redundancy: 1.6 % / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.045 / Rpim(I) all: 0.045 / Rrim(I) all: 0.064 / Χ2: 0.801 / Net I/σ(I): 7.2 / Num. measured all: 154794
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.34-2.381.70.646590.6880.9030.60.8480.44492.5
2.38-2.421.60.47247240.7770.9350.4720.6680.4192.5
2.42-2.471.60.40747570.8230.950.4070.5760.46693.4
2.47-2.521.60.31747680.9010.9740.3170.4480.42693.8
2.52-2.581.60.31247600.8580.9610.3120.4410.49292.6
2.58-2.641.60.28247320.880.9680.2820.3990.49393.4
2.64-2.71.60.24247320.910.9760.2420.3420.47293.5
2.7-2.771.60.19246710.9510.9870.1920.2710.4892.1
2.77-2.861.70.14648320.9590.9890.1460.2060.48694.4
2.86-2.951.70.11847820.9740.9930.1180.1670.54494
2.95-3.051.70.09848470.9680.9920.0980.1380.9494.7
3.05-3.181.70.07447760.9880.9970.0740.1040.62994.6
3.18-3.321.60.05748210.9920.9980.0570.0810.75394.2
3.32-3.51.60.04746450.9940.9990.0470.0660.69891.6
3.5-3.711.70.03748650.9950.9990.0370.0520.76595.1
3.71-41.70.03148110.9960.9990.0310.0431.10895.1
4-4.41.60.02847400.9960.9990.0280.0391.27593
4.4-5.041.60.02546740.9970.9990.0250.0361.31291.6
5.04-6.351.60.02548460.9960.9990.0250.0361.45695.2
6.35-501.60.02546380.9960.9990.0250.0362.61191.3

-
Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
SCALEPACKdata scaling
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→41.81 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.943 / SU B: 9.373 / SU ML: 0.195 / Cross valid method: THROUGHOUT / ESU R: 0.258 / ESU R Free: 0.2 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23004 4786 5 %RANDOM
Rwork0.208 ---
obs0.20911 90293 92.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 50.891 Å2
Baniso -1Baniso -2Baniso -3
1-0.31 Å20.05 Å2-0.12 Å2
2--0.01 Å2-0.06 Å2
3----0.1 Å2
Refinement stepCycle: 1 / Resolution: 2.35→41.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11130 0 0 296 11426
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.01211365
X-RAY DIFFRACTIONr_bond_other_d0.0120.01610406
X-RAY DIFFRACTIONr_angle_refined_deg0.9791.62815550
X-RAY DIFFRACTIONr_angle_other_deg0.4121.54324132
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.15151497
X-RAY DIFFRACTIONr_dihedral_angle_2_deg16.5959.953106
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.042101654
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0510.21807
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213351
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022145
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.365.2876000
X-RAY DIFFRACTIONr_mcbond_other2.365.2876000
X-RAY DIFFRACTIONr_mcangle_it3.7387.937493
X-RAY DIFFRACTIONr_mcangle_other3.7387.9317494
X-RAY DIFFRACTIONr_scbond_it2.2915.515365
X-RAY DIFFRACTIONr_scbond_other2.2915.5115362
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.7048.1988058
X-RAY DIFFRACTIONr_long_range_B_refined5.66373.06912270
X-RAY DIFFRACTIONr_long_range_B_other5.66273.08212228
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.35→2.408 Å
RfactorNum. reflection% reflection
Rfree0.37 297 -
Rwork0.38 5851 -
obs--81.56 %

+
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