[English] 日本語
Yorodumi
- PDB-6xjj: Structure of non-heme iron enzyme TropC: Radical tropolone biosyn... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6xjj
TitleStructure of non-heme iron enzyme TropC: Radical tropolone biosynthesis
Components2-oxoglutarate-dependent dioxygenase tropC
KeywordsOXIDOREDUCTASE / Tropolone
Function / homology
Function and homology information


Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen / dioxygenase activity / metal ion binding
Similarity search - Function
Non-haem dioxygenase N-terminal domain / non-haem dioxygenase in morphine synthesis N-terminal / 2OG-Fe(II) oxygenase superfamily / Isopenicillin N synthase-like superfamily / Oxoglutarate/iron-dependent dioxygenase / Fe(2+) 2-oxoglutarate dioxygenase domain profile.
Similarity search - Domain/homology
ACETATE ION / : / YTTRIUM (III) ION / 2-oxoglutarate-dependent dioxygenase tropC
Similarity search - Component
Biological speciesTalaromyces stipitatus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsMallik, L. / Doyon, T.J. / Narayan, A.R.H. / Koutmos, M.
CitationJournal: Chemrxiv / Year: 2020
Title: Radical Tropolone Biosynthesis
Authors: Doyon, T.J. / Skinner, K. / Yang, D. / Mallik, L. / Wymore, T. / Koutmos, M. / Zimmerman, P.M. / Narayan, A.
History
DepositionJun 24, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 2, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.journal_id_ISSN / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 2-oxoglutarate-dependent dioxygenase tropC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2674
Polymers40,0641
Non-polymers2043
Water905
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)111.014, 111.014, 89.889
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

-
Components

#1: Protein 2-oxoglutarate-dependent dioxygenase tropC / Tropolone synthesis protein C


Mass: 40063.512 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Talaromyces stipitatus (strain ATCC 10500 / CBS 375.48 / QM 6759 / NRRL 1006) (fungus)
Strain: ATCC 10500 / CBS 375.48 / QM 6759 / NRRL 1006 / Gene: tropC, tsR5, TSTA_117800 / Production host: Escherichia coli (E. coli)
References: UniProt: B8M9K5, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-YT3 / YTTRIUM (III) ION


Mass: 88.906 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Y
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / 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: 2.32 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 0.2 M Magnesium acetate, 20% PEG 8000, 0.01 M Yttrium (III) chloride hexahydrate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 17, 2018
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.7→48.07 Å / Num. obs: 17040 / % possible obs: 95.4 % / Redundancy: 5.9 % / Biso Wilson estimate: 64.9 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.034 / Rrim(I) all: 0.085 / Χ2: 1.01 / Net I/σ(I): 14.4
Reflection shellResolution: 2.7→2.873 Å / Redundancy: 6 % / Rmerge(I) obs: 1.073 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 2288 / CC1/2: 0.766 / Rpim(I) all: 0.72 / Rrim(I) all: 0.035 / Χ2: 1.04 / % possible all: 97.7

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5C3Q

5c3q


Resolution: 2.7→48.07 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2505 796 4.68 %0.25
Rwork0.2103 ---
obs0.2122 17015 94.89 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 64.9 Å2
Refinement stepCycle: LAST / Resolution: 2.7→48.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2308 0 6 5 2319
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052375
X-RAY DIFFRACTIONf_angle_d0.893221
X-RAY DIFFRACTIONf_dihedral_angle_d9.9411947
X-RAY DIFFRACTIONf_chiral_restr0.055345
X-RAY DIFFRACTIONf_plane_restr0.008419
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7001-2.86920.3741410.34962717X-RAY DIFFRACTION97
2.8692-3.09070.30871350.28882638X-RAY DIFFRACTION94
3.0907-3.40160.30831020.25282551X-RAY DIFFRACTION90
3.4016-3.89350.26991210.21752783X-RAY DIFFRACTION98
3.8935-4.90420.23821590.18152766X-RAY DIFFRACTION97
4.9042-42.390.21451380.18422764X-RAY DIFFRACTION93

+
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