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- PDB-9g88: Carotenoid cleavage oxygenase from Moesziomyces aphidis bound to ... -

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Basic information

Entry
Database: PDB / ID: 9g88
TitleCarotenoid cleavage oxygenase from Moesziomyces aphidis bound to acetate
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 / ACETATE ION / : / Lignostilbene dioxygenase
Function and homology information
Biological speciesMoesziomyces aphidis (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsPlewka, J. / Schober, L. / Magiera-Mularz, K. / Rudroff, F. / Winkler, M.
Funding support Austria, 1items
OrganizationGrant numberCountry
Austrian Science FundP33687 Austria
CitationJournal: To Be Published / Year: 2025
Title: structure of carotenoid cleavage oxygenase from Moesziomyces aphidis in apo and product bound forms
Authors: Schober, 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)126,0416
Polymers125,8112
Non-polymers2304
Water23,7801320
1
A: Lignostilbene dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,0203
Polymers62,9061
Non-polymers1152
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lignostilbene dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,0203
Polymers62,9061
Non-polymers1152
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.155, 85.957, 93.87
Angle α, β, γ (deg.)90, 100.336, 90
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A

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 asym-ID: A / Label asym-ID: A / Auth seq-ID: 24 - 548 / Label seq-ID: 32 - 556

Dom-ID
1
2

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

#1: Protein Lignostilbene dioxygenase / Carotenoid cleavage oxygenase


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-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2 / 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.: 1320 / 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: 2.28 Å3/Da / Density % sol: 45.96 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 20%w/vPolyethyleneglycol 3,350 200mM Lithiumacetate 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: Jun 5, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03322 Å / Relative weight: 1
ReflectionResolution: 1.4→46.17 Å / Num. obs: 216121 / % possible obs: 97.7 % / Redundancy: 3.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.048 / Rrim(I) all: 0.073 / Net I/σ(I): 9.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
7.67-46.173.90.03114220.9880.0290.043
1.4-1.423.11.00587290.4320.8511.325

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→46.17 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.965 / SU B: 1.246 / SU ML: 0.047 / Cross valid method: FREE R-VALUE / ESU R: 0.058 / ESU R Free: 0.061 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.1929 10853 5.029 %
Rwork0.1676 204975 -
all0.169 --
obs-215828 97.547 %
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: 21.317 Å2
Baniso -1Baniso -2Baniso -3
1--0.299 Å20 Å2-0.363 Å2
2--0.555 Å20 Å2
3----0.116 Å2
Refinement stepCycle: LAST / Resolution: 1.4→46.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8420 0 10 1320 9750
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0128734
X-RAY DIFFRACTIONr_angle_refined_deg1.9661.8311898
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.24151058
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.321556
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.682101366
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.74710432
X-RAY DIFFRACTIONr_chiral_restr0.1280.21223
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.027024
X-RAY DIFFRACTIONr_nbd_refined0.1970.24018
X-RAY DIFFRACTIONr_nbtor_refined0.3070.25873
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1130.21061
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1730.248
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1720.229
X-RAY DIFFRACTIONr_mcbond_it1.691.8254225
X-RAY DIFFRACTIONr_mcangle_it2.2953.2825284
X-RAY DIFFRACTIONr_scbond_it2.9972.0424509
X-RAY DIFFRACTIONr_scangle_it4.2463.646614
X-RAY DIFFRACTIONr_lrange_it5.24121.95513889
X-RAY DIFFRACTIONr_ncsr_local_group_10.0670.0517705
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.067490.05009
12AX-RAY DIFFRACTIONLocal ncs0.067490.05009
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.4360.3127100.3112700X-RAY DIFFRACTION82.3862
1.436-1.4760.2917650.28714781X-RAY DIFFRACTION97.5282
1.476-1.5180.2617940.25114538X-RAY DIFFRACTION99.3649
1.518-1.5650.2577580.23514204X-RAY DIFFRACTION99.4351
1.565-1.6160.227000.20513681X-RAY DIFFRACTION99.0768
1.616-1.6730.2236990.1913208X-RAY DIFFRACTION98.5683
1.673-1.7360.2026540.18312578X-RAY DIFFRACTION97.5308
1.736-1.8070.2086170.1712043X-RAY DIFFRACTION96.6043
1.807-1.8870.2096570.16511882X-RAY DIFFRACTION99.7772
1.887-1.9790.1966150.17111313X-RAY DIFFRACTION99.6908
1.979-2.0860.2085710.18210841X-RAY DIFFRACTION99.5725
2.086-2.2120.1915340.16610201X-RAY DIFFRACTION99.5826
2.212-2.3640.1965030.1629507X-RAY DIFFRACTION98.4364
2.364-2.5530.1824490.1538708X-RAY DIFFRACTION96.3996
2.553-2.7960.1784090.1548301X-RAY DIFFRACTION100
2.796-3.1250.1783910.1537501X-RAY DIFFRACTION99.7472
3.125-3.6050.1743640.1456620X-RAY DIFFRACTION99.5865
3.605-4.4090.163050.1265550X-RAY DIFFRACTION98.9354
4.409-6.2070.1512400.1434302X-RAY DIFFRACTION98.1205
6.207-46.170.2151180.2062516X-RAY DIFFRACTION99.9621

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