[English] 日本語
Yorodumi
- PDB-29lc: L-DOPA extradiol dioxygenase from Beta vulgaris in complex with m... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 29lc
TitleL-DOPA extradiol dioxygenase from Beta vulgaris in complex with mimosine
Components4,5-DOPA dioxygenase extradiol 1
KeywordsOXIDOREDUCTASE / DODA / betalamic acid / beta vulgaris / L-DOPA extradiol dioxygenase / mimosine
Function / homology
Function and homology information


stizolobate synthase / stizolobate synthase activity / ferrous iron binding / zinc ion binding
Similarity search - Function
Extradiol aromatic ring-opening dioxygenase, DODA-type / Extradiol ring-cleavage dioxygenase, class III enzyme, subunit B / Catalytic LigB subunit of aromatic ring-opening dioxygenase
Similarity search - Domain/homology
MIMOSINE / NICKEL (II) ION / DI(HYDROXYETHYL)ETHER / 4,5-DOPA dioxygenase extradiol 1
Similarity search - Component
Biological speciesBeta vulgaris (beet)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.46 Å
AuthorsHapke, M. / Kluza, A. / Seweryn-Ozog, K. / Andrys-Olek, J. / Milaczewska-Kregiel, A.M. / Borowski, T.
Funding support Poland, 1items
OrganizationGrant numberCountry
Polish National Science Centre2022/45/B/ST4/01411 Poland
CitationJournal: To Be Published
Title: Structural and mechanistic insight into oxidative ring opening catalyzed by L-DOPA extradiol dioxygenase from Beta vulgaris
Authors: Hapke, M. / Kluza, A. / Seweryn-Ozog, K. / Andrys-Olek, J. / Milaczewska, A.M. / Borowski, T.
History
DepositionMar 19, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 12, 2026Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 4,5-DOPA dioxygenase extradiol 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1499
Polymers31,4761
Non-polymers6738
Water4,342241
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1590 Å2
ΔGint5 kcal/mol
Surface area12170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.440, 58.360, 53.190
Angle α, β, γ (deg.)90.000, 109.180, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein 4,5-DOPA dioxygenase extradiol 1


Mass: 31475.656 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Beta vulgaris (beet) / Gene: DODA1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: I3PFJ9, stizolobate synthase

-
Non-polymers , 5 types, 249 molecules

#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-MMS / MIMOSINE / 3-HYDROXY-4-OXO-1(4H)-PYRIDINEALANINE


Mass: 198.176 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10N2O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 241 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.18 Å3/Da / Density % sol: 43.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 30 mM magnesium chloride, 0.2 M ammonium sulphate, 0.1 M MES pH 6.5, 30% PEG 5000 MME

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 5, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.46→43.86 Å / Num. obs: 46189 / % possible obs: 98.9 % / Redundancy: 6.8 % / Biso Wilson estimate: 27.1 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.168 / Net I/σ(I): 11.7
Reflection shellResolution: 1.46→1.55 Å / Redundancy: 6.8 % / Mean I/σ(I) obs: 1 / Num. unique obs: 7425 / CC1/2: 0.671 / Rrim(I) all: 2.049 / % possible all: 99

-
Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
MxCuBEdata collection
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.46→28.7 Å / SU ML: 0.2294 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.1385
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1939 2098 4.55 %
Rwork0.1574 43995 -
obs0.1591 46093 98.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.93 Å2
Refinement stepCycle: LAST / Resolution: 1.46→28.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2181 0 42 241 2464
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082362
X-RAY DIFFRACTIONf_angle_d0.89133222
X-RAY DIFFRACTIONf_chiral_restr0.0765335
X-RAY DIFFRACTIONf_plane_restr0.0083418
X-RAY DIFFRACTIONf_dihedral_angle_d13.2681849
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.46-1.490.57751400.47062934X-RAY DIFFRACTION98.91
1.49-1.530.36011380.37472890X-RAY DIFFRACTION98.66
1.53-1.570.33821390.29592917X-RAY DIFFRACTION98.8
1.57-1.620.29491380.23522888X-RAY DIFFRACTION97.3
1.62-1.670.27431380.21952911X-RAY DIFFRACTION98.96
1.67-1.730.23351400.20352932X-RAY DIFFRACTION99.06
1.73-1.80.23641400.17912931X-RAY DIFFRACTION99.32
1.8-1.880.22171400.14162934X-RAY DIFFRACTION98.97
1.88-1.980.1841400.13162933X-RAY DIFFRACTION99.32
1.98-2.110.181410.13392955X-RAY DIFFRACTION98.88
2.11-2.270.18421370.13832875X-RAY DIFFRACTION97.44
2.27-2.50.19021420.13482967X-RAY DIFFRACTION99.49
2.5-2.860.1471400.13292953X-RAY DIFFRACTION99.36
2.86-3.60.15961430.13362984X-RAY DIFFRACTION99.11
3.6-28.70.17011420.14522991X-RAY DIFFRACTION98.37

+
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