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- PDB-9m3e: Carotenoid Cleavage Dioxygenase 1 variant from Osmanthus fragrans... -

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Basic information

Entry
Database: PDB / ID: 9m3e
TitleCarotenoid Cleavage Dioxygenase 1 variant from Osmanthus fragrans A191G E408Q
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: 2.5 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
DepositionMar 1, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 4, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)63,92811
Polymers61,3521
Non-polymers2,57610
Water4,360242
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 area21910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)209.802, 209.802, 209.802
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number213
Space group name H-MP4132

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Components

#1: Protein carotenoid 9,10-dioxygenase


Mass: 61352.340 Da / Num. of mol.: 1 / Mutation: A191G/E408Q
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, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; Miscellaneous
#2: 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 / Feature type: SUBJECT OF INVESTIGATION / Comment: detergent*YM
#3: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 242 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 6.27 Å3/Da / Density % sol: 80.39 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: Tris pH 7.5, (NH4)2SO4

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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: 2.5→49.45 Å / Num. obs: 54893 / % possible obs: 100 % / Redundancy: 82.5 % / CC1/2: 0.998 / Net I/σ(I): 13.4
Reflection shellResolution: 2.5→2.57 Å / Mean I/σ(I) obs: 1.3 / Num. unique obs: 4413 / CC1/2: 0.446

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Processing

Software
NameVersionClassification
PHENIX1.20.1refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→49.45 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 20.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2128 2712 4.94 %
Rwork0.1827 --
obs0.1841 54891 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→49.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4332 0 31 242 4605
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084475
X-RAY DIFFRACTIONf_angle_d0.9856059
X-RAY DIFFRACTIONf_dihedral_angle_d13.91682
X-RAY DIFFRACTIONf_chiral_restr0.059643
X-RAY DIFFRACTIONf_plane_restr0.007771
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.550.3441380.28992699X-RAY DIFFRACTION100
2.55-2.590.30371360.28172693X-RAY DIFFRACTION100
2.59-2.650.34291450.27142702X-RAY DIFFRACTION100
2.65-2.70.31831490.25642678X-RAY DIFFRACTION100
2.71-2.770.28681340.23342708X-RAY DIFFRACTION100
2.77-2.840.25241450.23062708X-RAY DIFFRACTION100
2.84-2.910.2581430.2222727X-RAY DIFFRACTION100
2.91-30.30551590.20952668X-RAY DIFFRACTION100
3-3.10.22411440.19752700X-RAY DIFFRACTION100
3.1-3.210.19761440.19342726X-RAY DIFFRACTION100
3.21-3.340.18221290.18462745X-RAY DIFFRACTION100
3.34-3.490.21391270.17432740X-RAY DIFFRACTION100
3.49-3.670.22591500.16982737X-RAY DIFFRACTION100
3.67-3.90.18771300.15322757X-RAY DIFFRACTION100
3.9-4.20.17661510.15722756X-RAY DIFFRACTION100
4.2-4.620.14411450.13992760X-RAY DIFFRACTION100
4.62-5.290.18071280.14752826X-RAY DIFFRACTION100
5.29-6.660.20621400.19282841X-RAY DIFFRACTION100
6.67-49.450.21951750.19043008X-RAY DIFFRACTION100

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