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- PDB-9g8f: Carotenoid cleavage oxygenase from Moesziomyces aphidis bound to ... -

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Basic information

Entry
Database: PDB / ID: 9g8f
TitleCarotenoid cleavage oxygenase from Moesziomyces aphidis bound to orto vanillin
ComponentsLignostilbene dioxygenase
KeywordsMETAL BINDING PROTEIN / oxygenase / Moesziomyces aphidis
Function / homologycarotenoid dioxygenase activity / carotene catabolic process / Carotenoid oxygenase / Retinal pigment epithelial membrane protein / metal ion binding / : / : / Lignostilbene dioxygenase
Function and homology information
Biological speciesMoesziomyces aphidis (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.844 Å
AuthorsPlewka, J. / Schorber, 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: Schorber, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)126,2276
Polymers125,8112
Non-polymers4164
Water17,943996
1
A: Lignostilbene dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,1143
Polymers62,9061
Non-polymers2082
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lignostilbene dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,1143
Polymers62,9061
Non-polymers2082
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.883, 84.937, 107.02
Angle α, β, γ (deg.)90, 108.399, 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)

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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-V9L / ortho-vanillin / 3-methoxy-2-oxidanyl-benzaldehyde / 2-hydroxy-3-methoxybenzaldehyde


Mass: 152.147 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 996 / 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: 2.46 Å3/Da / Density % sol: 50.08 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.2M Sodium acetate trihydrate 0.1M Sodium HEPES 7.525% w/v PEG 3350

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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: 1.84→48.76 Å / Num. obs: 101754 / % possible obs: 96.8 % / Redundancy: 6.5 % / CC1/2: 0.99 / Rmerge(I) obs: 0.154 / Rpim(I) all: 0.099 / Rrim(I) all: 0.184 / Χ2: 0.98 / Net I/σ(I): 9.5
Reflection shell

Redundancy: 6.5 %

Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
10.1-48.760.08817.86810.9940.0540.1031.0298.9
1.84-1.880.618431180.9190.3940.7350.660.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.844→48.76 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.881 / SU B: 3.507 / SU ML: 0.109 / Cross valid method: FREE R-VALUE / ESU R: 0.16 / ESU R Free: 0.154 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2593 5064 4.995 %
Rwork0.2095 96311 -
all0.212 --
obs-101375 96.338 %
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: 20.601 Å2
Baniso -1Baniso -2Baniso -3
1--1.085 Å20 Å20.903 Å2
2---0.462 Å20 Å2
3---0.774 Å2
Refinement stepCycle: LAST / Resolution: 1.844→48.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8420 0 24 996 9440
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0128706
X-RAY DIFFRACTIONr_angle_refined_deg2.3441.8211850
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.96151048
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.327660
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.668101358
X-RAY DIFFRACTIONr_dihedral_angle_6_deg13.83110430
X-RAY DIFFRACTIONr_chiral_restr0.1640.21216
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.026978
X-RAY DIFFRACTIONr_nbd_refined0.2120.24446
X-RAY DIFFRACTIONr_nbtor_refined0.3050.25808
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2030.21036
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2070.254
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1290.221
X-RAY DIFFRACTIONr_mcbond_it2.4761.8384198
X-RAY DIFFRACTIONr_mcangle_it3.1973.2955244
X-RAY DIFFRACTIONr_scbond_it3.3212.0244508
X-RAY DIFFRACTIONr_scangle_it4.3853.6196606
X-RAY DIFFRACTIONr_lrange_it6.38221.45514228
X-RAY DIFFRACTIONr_ncsr_local_group_10.0770.0517538
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.077110.05008
12BX-RAY DIFFRACTIONLocal ncs0.077110.05008
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
1.844-1.8920.282900.21854200.22177360.9470.96873.81080.2
1.892-1.9430.2823610.20771470.21175450.9450.97199.50960.19
1.943-20.2653810.2168800.21373070.9520.96999.37050.192
2-2.0610.2712710.2168350.21271660.9510.96999.16270.194
2.061-2.1290.2453200.19764560.19968800.9560.97398.48840.183
2.129-2.2030.2563500.19762320.266910.9550.97398.37090.184
2.203-2.2860.2683480.20759970.21164780.9510.96997.94690.194
2.286-2.3790.2873370.21956990.22362050.9460.96797.27640.205
2.379-2.4850.2882780.22654220.22959830.9470.96395.26990.212
2.485-2.6060.2853080.21553400.21856960.9440.9799.15730.209
2.606-2.7460.2622800.20951310.21254470.9570.97199.33910.204
2.746-2.9120.2872870.21947910.22351330.9480.96898.92850.219
2.912-3.1130.2662290.2245430.22248460.950.96798.4730.222
3.113-3.3610.2711910.21942570.22245160.9550.96698.49420.224
3.361-3.680.2492180.21538220.21741400.9580.96797.58450.22
3.68-4.1110.2561650.21834400.2237660.9530.96695.72490.231
4.111-4.7420.2051530.19429040.19533590.9670.97391.00920.207
4.742-5.7940.2241500.19326490.19528200.9660.97399.25530.208
5.794-8.1360.251890.19421250.19622240.9610.97499.55040.213
8.136-48.760.189580.18812210.18812820.9750.97799.7660.214

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