[English] 日本語
Yorodumi
- PDB-9luz: Carotenoid Cleavage Dioxygenase 1 from Osmanthus fragrans -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9luz
TitleCarotenoid Cleavage Dioxygenase 1 from Osmanthus fragrans
Componentscarotenoid 9,10-dioxygenase
KeywordsPLANT PROTEIN / Biosynthesis of ionone / CCD1
Function / homology: / carotenoid dioxygenase activity / carotene catabolic process / Carotenoid oxygenase / Retinal pigment epithelial membrane protein / chloroplast stroma / metal ion binding / NICKEL (II) ION / carotenoid 9,10-dioxygenase
Function and homology information
Biological speciesOsmanthus fragrans (sweet osmanthus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsSharma, D. / Xue, B.
Funding support Singapore, 1items
OrganizationGrant numberCountry
Ministry of Education (MoE, Singapore) Singapore
CitationJournal: To Be Published
Title: Structure-based Enzyme Engineering of CCD1 to Improve Substrate Specificity for beta-ionone Biosynthesis
Authors: Sharma, D. / Xue, B. / Esque, E. / Bozonnet, S. / Ong, J.S. / Yew, W.S. / Remaud-Simeon, M. / Andre, I. / Chen, X.
History
DepositionFeb 10, 2025Deposition site: PDBJ / Processing site: PDBJ
SupersessionFeb 11, 2026ID: 7VUD
Revision 1.0Feb 11, 2026Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: carotenoid 9,10-dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,94311
Polymers61,3671
Non-polymers2,57610
Water4,738263
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area200 Å2
ΔGint-16 kcal/mol
Surface area21850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)210.242, 210.242, 210.242
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number213
Space group name H-MP4132

-
Components

#1: Protein carotenoid 9,10-dioxygenase


Mass: 61367.348 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Osmanthus fragrans (sweet osmanthus) / Gene: CCD1 / Production host: Escherichia coli (E. coli) / References: UniProt: D4QE74
#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-OXN / OXTOXYNOL-10 / ALPHA-[4-(1,1,3,3-TETRAMETHYLBUTYL)PHENYL]-OMEGA-HYDROXYPOLY(OXY-1,2-ETHANEDIYL) / TRITON X-100


Mass: 646.849 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C34H62O11 / Comment: detergent*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 263 / 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: 6.31 Å3/Da / Density % sol: 80.51 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: Tris pH 7.5, (NH4)2SO4

-
Data collection

DiffractionMean temperature: 98.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95365 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 3, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95365 Å / Relative weight: 1
ReflectionResolution: 2.3→48.3 Å / Num. obs: 70655 / % possible obs: 99.98 % / Redundancy: 3.6 % / CC1/2: 0.999 / Net I/σ(I): 17.5
Reflection shellResolution: 2.3→2.35 Å / Rmerge(I) obs: 1.2 / Num. unique obs: 4480 / CC1/2: 0.429 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→48.279 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.946 / WRfactor Rfree: 0.196 / WRfactor Rwork: 0.177 / Average fsc free: 0.9641 / Average fsc work: 0.9663 / Cross valid method: THROUGHOUT / ESU R: 0.137 / ESU R Free: 0.128
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2093 3143 4.455 %RANDOM
Rwork0.1911 67408 --
all0.192 ---
obs-70551 99.977 %-
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: 47.863 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.3→48.279 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4261 0 103 263 4627
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0124469
X-RAY DIFFRACTIONr_bond_other_d0.0020.0164124
X-RAY DIFFRACTIONr_angle_refined_deg1.4471.6566050
X-RAY DIFFRACTIONr_angle_other_deg0.7451.5679614
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0945534
X-RAY DIFFRACTIONr_dihedral_angle_2_deg3.891520
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.79810753
X-RAY DIFFRACTIONr_dihedral_angle_6_deg17.7110200
X-RAY DIFFRACTIONr_chiral_restr0.0640.2649
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024941
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02891
X-RAY DIFFRACTIONr_nbd_refined0.2070.2694
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2210.23813
X-RAY DIFFRACTIONr_nbtor_refined0.1850.22123
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0920.22329
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1330.2224
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1250.213
X-RAY DIFFRACTIONr_nbd_other0.1980.255
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1510.212
X-RAY DIFFRACTIONr_mcbond_it2.4055.132139
X-RAY DIFFRACTIONr_mcbond_other2.4055.132139
X-RAY DIFFRACTIONr_mcangle_it3.7697.6782672
X-RAY DIFFRACTIONr_mcangle_other3.7687.682673
X-RAY DIFFRACTIONr_scbond_it3.9655.3962330
X-RAY DIFFRACTIONr_scbond_other3.9645.3952331
X-RAY DIFFRACTIONr_scangle_it5.6367.9773378
X-RAY DIFFRACTIONr_scangle_other5.6887.9753379
X-RAY DIFFRACTIONr_lrange_it6.55764.5274733
X-RAY DIFFRACTIONr_lrange_other6.55764.5274734
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc workWRfactor RworkFsc free
2.3-2.3600.29451000.29451000.9320.294
2.36-2.4240.305850.28349100.28349950.9410.280.929
2.424-2.4940.3012620.27945890.28148510.950.270.945
2.494-2.5710.2572300.25545010.25547310.9570.2430.956
2.571-2.6550.2582300.23843540.23945840.9620.220.954
2.655-2.7480.2662470.22741940.2344410.9660.2030.955
2.748-2.8510.2482200.21940950.2243150.9680.1920.96
2.851-2.9670.2631800.21539560.21741360.970.1870.958
2.967-3.0990.2272080.20137720.20239800.9740.1740.965
3.099-3.2490.2222050.19635930.19837980.9750.1750.966
3.249-3.4240.2491880.19134680.19436560.9770.1740.958
3.424-3.6310.2041650.18132940.18334590.980.1690.978
3.631-3.880.1891450.16230940.16332390.9840.1540.979
3.88-4.1890.1771520.15829090.15930610.9850.1540.98
4.189-4.5850.1561650.14226450.14328100.9870.1440.987
4.585-5.120.1471220.14224550.14225770.9870.1480.989
5.12-5.9010.1631090.17321720.17222810.9820.1770.984
5.901-7.2010.2431100.20518660.20719760.9760.210.967
7.201-10.0720.198800.16714980.16815780.9820.1840.979
10.072-48.2790.248400.2429430.2429830.9480.2590.947

+
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