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- PDB-8fu5: Crystal structure of Fe-CAO1 in complex with piceatannol -

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Basic information

Entry
Database: PDB / ID: 8fu5
TitleCrystal structure of Fe-CAO1 in complex with piceatannol
ComponentsCarotenoid oxygenase
KeywordsOXIDOREDUCTASE/SUBSTRATE / non-heme iron / beta propeller / stilbene / dioxygenase / oxidoreductase / OXIDOREDUCTASE-SUBSTRATE complex
Function / homologyCarotenoid oxygenase / Retinal pigment epithelial membrane protein / oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen / metal ion binding / BENZOIC ACID / : / PICEATANNOL / Carotenoid oxygenase
Function and homology information
Biological speciesNeurospora crassa (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.01 Å
AuthorsKiser, P.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE-2107713 United States
CitationJournal: To Be Published
Title: Crystal structure of Fe-CAO1 in complex with piceatannol
Authors: Kiser, P.D.
History
DepositionJan 16, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Carotenoid oxygenase
B: Carotenoid oxygenase
C: Carotenoid oxygenase
D: Carotenoid oxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)239,68116
Polymers237,9924
Non-polymers1,68912
Water36,4442023
1
A: Carotenoid oxygenase
D: Carotenoid oxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,8408
Polymers118,9962
Non-polymers8446
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Carotenoid oxygenase
C: Carotenoid oxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,8408
Polymers118,9962
Non-polymers8446
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)101.192, 101.192, 449.357
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein
Carotenoid oxygenase


Mass: 59497.934 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neurospora crassa (fungus) / Gene: GE21DRAFT_6499 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0B0DIC8
#2: Chemical
ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-PIT / PICEATANNOL / 4-[(E)-2-(3,5-DIHYDROXYPHENYL)ETHENYL]BENZENE-1,2-DIOL


Mass: 244.243 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H12O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-BEZ / BENZOIC ACID


Mass: 122.121 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C7H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2023 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.79 Å3/Da / Density % sol: 55.92 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1 M HEPES-NaOH pH 7, 42% sodium polyacrylate 2100

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 29, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.01→50 Å / Num. obs: 179310 / % possible obs: 99.8 % / Redundancy: 6.8 % / CC1/2: 0.996 / Rmerge(I) obs: 0.234 / Net I/σ(I): 10.54
Reflection shellResolution: 2.01→2.13 Å / Redundancy: 6.8 % / Rmerge(I) obs: 2.067 / Mean I/σ(I) obs: 1.18 / Num. unique obs: 28387 / CC1/2: 0.456 / % possible all: 99.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0403refinement
XDSdata reduction
XDSdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.01→49.36 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.958 / SU B: 4.756 / SU ML: 0.118 / Cross valid method: THROUGHOUT / ESU R: 0.15 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19578 7839 4.4 %RANDOM
Rwork0.1707 ---
obs0.17183 171471 99.77 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.755 Å2
Baniso -1Baniso -2Baniso -3
1-0.49 Å20.24 Å20 Å2
2--0.49 Å2-0 Å2
3----1.58 Å2
Refinement stepCycle: 1 / Resolution: 2.01→49.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15942 0 112 2023 18077
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.01216846
X-RAY DIFFRACTIONr_bond_other_d0.0010.01615204
X-RAY DIFFRACTIONr_angle_refined_deg1.0461.65322938
X-RAY DIFFRACTIONr_angle_other_deg0.3631.57435104
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.38252044
X-RAY DIFFRACTIONr_dihedral_angle_2_deg4.2049.685254
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.02810.6862603
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.43515119
X-RAY DIFFRACTIONr_chiral_restr0.0520.22311
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0219610
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024123
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7823.228101
X-RAY DIFFRACTIONr_mcbond_other1.7823.228101
X-RAY DIFFRACTIONr_mcangle_it2.745.77910170
X-RAY DIFFRACTIONr_mcangle_other2.7415.77910171
X-RAY DIFFRACTIONr_scbond_it2.4413.5088745
X-RAY DIFFRACTIONr_scbond_other2.443.5098746
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.0326.31312769
X-RAY DIFFRACTIONr_long_range_B_refined6.06437.7119226
X-RAY DIFFRACTIONr_long_range_B_other6.04837.5819183
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.01→2.059 Å
RfactorNum. reflection% reflection
Rfree0.383 629 -
Rwork0.354 12313 -
obs--98.33 %

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