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- PDB-9g8a: Carotenoid cleavage oxygenase from Moesziomyces aphidis bound to ... -

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Basic information

Entry
Database: PDB / ID: 9g8a
TitleCarotenoid cleavage oxygenase from Moesziomyces aphidis bound to p-hydroxybenzaldehyde
ComponentsLignostilbene dioxygenase
KeywordsMETAL BINDING PROTEIN / oxygenase / Moesziomyces aphidi / p-hydroxybenzaldehyde
Function / homologycarotenoid dioxygenase activity / carotene catabolic process / Carotenoid oxygenase / Retinal pigment epithelial membrane protein / metal ion binding / : / P-HYDROXYBENZALDEHYDE / Lignostilbene dioxygenase
Function and homology information
Biological speciesMoesziomyces aphidis (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)126,1676
Polymers125,8112
Non-polymers3564
Water15,745874
1
A: Lignostilbene dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,0843
Polymers62,9061
Non-polymers1782
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lignostilbene dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,0843
Polymers62,9061
Non-polymers1782
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.836, 83.808, 98.117
Angle α, β, γ (deg.)90, 104.498, 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-HBA / P-HYDROXYBENZALDEHYDE


Mass: 122.121 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H6O2 / 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.: 874 / 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: 2.27 Å3/Da / Density % sol: 45.88 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 20% w/v Polyethyleneglycol 3,350 200mM Ammonium acetate 30% GOL

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.87313 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 4, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87313 Å / Relative weight: 1
ReflectionResolution: 2→69.55 Å / Num. obs: 67761 / % possible obs: 89.1 % / Redundancy: 3 % / CC1/2: 0.989 / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.11 / Rrim(I) all: 0.156 / Χ2: 0.48 / Net I/σ(I): 4.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
9.38-69.552.80.03313.27270.9960.0330.0470.3892.7
2-2.053.10.4521.549900.7310.4430.6330.4397.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→69.548 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.937 / SU B: 5.481 / SU ML: 0.144 / Cross valid method: FREE R-VALUE / ESU R: 0.223 / ESU R Free: 0.176 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2181 3363 4.965 %
Rwork0.1799 64377 -
all0.182 --
obs-67740 88.916 %
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: 23.128 Å2
Baniso -1Baniso -2Baniso -3
1--1.511 Å2-0 Å2-1.167 Å2
2--1.081 Å20 Å2
3---0.911 Å2
Refinement stepCycle: LAST / Resolution: 2→69.548 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8420 0 20 874 9314
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0128702
X-RAY DIFFRACTIONr_angle_refined_deg2.1931.82111844
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.76551048
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.73558
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.855101358
X-RAY DIFFRACTIONr_dihedral_angle_6_deg13.51510430
X-RAY DIFFRACTIONr_chiral_restr0.1720.21216
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.026976
X-RAY DIFFRACTIONr_nbd_refined0.1340.23876
X-RAY DIFFRACTIONr_nbtor_refined0.260.25649
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0830.2907
X-RAY DIFFRACTIONr_metal_ion_refined0.1850.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1290.268
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1140.223
X-RAY DIFFRACTIONr_mcbond_it1.5412.1374198
X-RAY DIFFRACTIONr_mcangle_it2.3573.8645244
X-RAY DIFFRACTIONr_scbond_it2.4182.3044504
X-RAY DIFFRACTIONr_scangle_it3.7294.1576600
X-RAY DIFFRACTIONr_lrange_it5.59625.50913380
X-RAY DIFFRACTIONr_ncsr_local_group_10.0450.0517397
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.044890.05009
12BX-RAY DIFFRACTIONLocal ncs0.044890.05009
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
2-2.0520.2632630.25551820.25656150.950.95196.97240.251
2.052-2.1080.2531520.23331280.23454300.9570.96160.40520.227
2.108-2.1690.252790.22548840.22653280.9570.96696.90320.219
2.169-2.2360.2532490.21647220.21851300.9610.96896.90060.209
2.236-2.3090.2721550.21434430.21650280.9470.96971.55930.206
2.309-2.390.2662050.19944980.20248660.9550.97396.65020.192
2.39-2.480.2622460.2142760.21346620.9530.97196.9970.202
2.48-2.5810.2541980.241620.20345000.9620.97496.88890.191
2.581-2.6960.2571470.20429730.20743340.9590.97571.98890.195
2.696-2.8270.2281830.18537650.18741130.9660.97895.98830.177
2.827-2.980.2482100.18635910.1939470.9580.97996.3010.181
2.98-3.160.2141810.17533670.17737280.9690.98195.17170.17
3.16-3.3780.2081880.17931520.1835010.9720.98195.40130.177
3.378-3.6480.1971200.16523540.16632700.9770.98475.65750.164
3.648-3.9950.1891190.15219400.15430100.9830.98668.40530.153
3.995-4.4650.1741400.13125090.13327280.9860.99197.10410.137
4.465-5.1520.1551060.12122610.12224180.9880.99297.89080.127
5.152-6.3010.173960.14618740.14720280.9840.98897.140.151
6.301-8.8750.2720.15714930.15816240.9740.98696.3670.164
8.875-69.5480.195540.1958040.1959240.9780.97392.85710.222

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