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- PDB-9g89: Carotenoid cleavage oxygenase from Moesziomyces aphidis bound to ... -

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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: Structural and Functional Characteristics of Potent Dioxygenase from Moesziomyces aphidis .
Authors: Schober, L. / Plewka, J. / Sriwaiyaphram, K. / Bielec, B. / Schiefer, A. / Wongnate, T. / 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
Revision 1.1Aug 13, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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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)126,78012
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)

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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-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

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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: 2.44 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

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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: 1.67→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

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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

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