[English] 日本語
Yorodumi
- PDB-9g89: Carotenoid cleavage oxygenase from Moesziomyces aphidis bound to ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9g89
TitleCarotenoid cleavage oxygenase from Moesziomyces aphidis bound to vanillin
ComponentsLignostilbene dioxygenase
KeywordsMETAL BINDING PROTEIN / oxygenase / Moesziomyces aphidis / vanillin
Function / homologycarotenoid dioxygenase activity / carotene catabolic process / Carotenoid oxygenase / Retinal pigment epithelial membrane protein / metal ion binding / : / 4-hydroxy-3-methoxybenzaldehyde / Lignostilbene dioxygenase
Function and homology information
Biological speciesMoesziomyces aphidis (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.671 Å
AuthorsPlewka, J. / Schober, L. / Magiera-Mularz, K. / Rudroff, F. / Winkler, M.
Funding support Austria, 1items
OrganizationGrant numberCountry
Austrian Science FundP33687 Austria
CitationJournal: Jacs Au / Year: 2025
Title: structure of carotenoid cleavage oxygenase from Moesziomyces aphidis in apo and product bound forms
Authors: Schober, L. / Plewka, J. / Magiera-Mularz, K. / Rudroff, F. / Winkler, M.
History
DepositionJul 23, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 25, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Lignostilbene dioxygenase
B: Lignostilbene dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,78012
Polymers125,8112
Non-polymers96910
Water16,087893
1
A: Lignostilbene dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,5748
Polymers62,9061
Non-polymers6687
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lignostilbene dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,2064
Polymers62,9061
Non-polymers3003
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.68, 84.676, 106.571
Angle α, β, γ (deg.)90, 108.349, 90
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: TYR / Beg label comp-ID: TYR / End auth comp-ID: ALA / End label comp-ID: ALA / Auth seq-ID: 24 - 548 / Label seq-ID: 32 - 556

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

-
Components

#1: Protein Lignostilbene dioxygenase / Carotenoid cleavage oxygenase / Aromatic dioxygenase


Mass: 62905.562 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Aromatic dioxygenase / Source: (gene. exp.) Moesziomyces aphidis (fungus) / Gene: PaG_05861 / Production host: Escherichia coli (E. coli) / References: UniProt: W3VHW6
#2: Chemical ChemComp-V55 / 4-hydroxy-3-methoxybenzaldehyde / p-vanillin


Mass: 152.147 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 893 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.44 Å3/Da / Density % sol: 49.59 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 0.1MPCTP 7.0 25% w/v PEG 1500 30% GOL

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.03322 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 18, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03322 Å / Relative weight: 1
ReflectionResolution: 1.67→48.56 Å / Num. obs: 137992 / % possible obs: 98.8 % / Redundancy: 6.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.054 / Rrim(I) all: 0.103 / Χ2: 1.01 / Net I/σ(I): 12.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
9.15-48.566.70.03347.18920.9990.020.0391.0699
1.67-1.771.4731.267960.5280.9111.7370.9698.4

-
Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.671→48.56 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.961 / SU B: 2.235 / SU ML: 0.07 / Cross valid method: FREE R-VALUE / ESU R: 0.088 / ESU R Free: 0.089 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.1944 6946 5.036 %
Rwork0.1629 130977 -
all0.164 --
obs-137923 98.667 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 26.999 Å2
Baniso -1Baniso -2Baniso -3
1--0.636 Å20 Å20.811 Å2
2--0.514 Å20 Å2
3----0.342 Å2
Refinement stepCycle: LAST / Resolution: 1.671→48.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8406 0 60 893 9359
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0128733
X-RAY DIFFRACTIONr_angle_refined_deg1.9191.8211877
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.50251050
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.176660
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.521101357
X-RAY DIFFRACTIONr_dihedral_angle_6_deg13.96210429
X-RAY DIFFRACTIONr_chiral_restr0.1240.21223
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.026977
X-RAY DIFFRACTIONr_nbd_refined0.1910.24250
X-RAY DIFFRACTIONr_nbtor_refined0.3060.25922
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.2957
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1940.265
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.3240.223
X-RAY DIFFRACTIONr_mcbond_it2.2662.434203
X-RAY DIFFRACTIONr_mcangle_it3.014.3575252
X-RAY DIFFRACTIONr_scbond_it3.532.694530
X-RAY DIFFRACTIONr_scangle_it4.8774.7926625
X-RAY DIFFRACTIONr_lrange_it5.76528.51114062
X-RAY DIFFRACTIONr_ncsr_local_group_10.0620.0517841
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.061520.05009
12BX-RAY DIFFRACTIONLocal ncs0.061520.05009
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.671-1.7150.3035340.28595990.286102770.9350.93998.59880.275
1.715-1.7610.2984670.26994650.271100150.9370.94899.17120.254
1.761-1.8120.2765060.24491330.24597720.9470.95998.6390.225
1.812-1.8680.264380.22587620.22794600.9570.96597.25160.201
1.868-1.9290.2184270.285540.20192030.9680.97497.58770.175
1.929-1.9970.2143960.17984230.18188850.9720.9899.25720.157
1.997-2.0720.1974560.16780390.16885620.9760.98399.21750.144
2.072-2.1570.1864350.16177710.16282450.9780.98499.5270.14
2.157-2.2520.1924350.15774950.15979740.9770.98599.44820.135
2.252-2.3620.1913840.1571590.15276000.9780.98699.250.129
2.362-2.4890.223650.16167640.16472120.9710.98498.84910.14
2.489-2.640.2133120.16863010.1768500.9740.98496.54010.147
2.64-2.8220.1933200.15359910.15564020.9780.98698.57860.137
2.822-3.0470.183030.15356370.15559840.9810.98699.26470.14
3.047-3.3360.1752770.1551880.15155110.9810.98699.16530.142
3.336-3.7280.1672620.14747210.14850210.9830.98799.24320.145
3.728-4.30.1691960.13241950.13344180.9840.9999.38890.137
4.3-5.2570.1681980.1333930.13237610.9860.99195.47990.14
5.257-7.3910.1831520.15627830.15729360.9830.98799.96590.164
7.391-48.560.163830.15216040.15316900.9830.98799.82250.164

+
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