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- PDB-8srl: Crystal structure of T151V CAO1 in complex with piceatannol -

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Basic information

Entry
Database: PDB / ID: 8srl
TitleCrystal structure of T151V CAO1 in complex with piceatannol
ComponentsCarotenoid oxygenase
KeywordsOXIDOREDUCTASE / non-heme iron / beta propeller / stilbene / mutant
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 CAO1
Authors: Kiser, P.D.
History
DepositionMay 5, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)239,67316
Polymers237,9844
Non-polymers1,68912
Water36,0482001
1
A: Carotenoid oxygenase
D: Carotenoid oxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,8368
Polymers118,9922
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)119,8368
Polymers118,9922
Non-polymers8446
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.888, 100.888, 448.169
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: 59495.965 Da / Num. of mol.: 4 / Mutation: T151V
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 / Piceatannol


Mass: 244.243 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C14H12O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-BEZ / BENZOIC ACID / Benzoic acid


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


Mass: 18.015 Da / Num. of mol.: 2001 / 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: 2.8 Å3/Da / Density % sol: 56.07 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 42% sodium polyacrylate 2100 0.05 M HEPES-NaOH pH 7

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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: Feb 12, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.01→50.13 Å / Num. obs: 177907 / % possible obs: 99.9 % / Redundancy: 10.1 % / CC1/2: 0.998 / Rmerge(I) obs: 0.152 / Net I/σ(I): 12.77
Reflection shellResolution: 2.01→2.13 Å / Rmerge(I) obs: 2.377 / Num. unique obs: 28339 / CC1/2: 0.413 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0405refinement
XDSdata reduction
XDSdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.01→50.13 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.963 / SU B: 4.846 / SU ML: 0.119 / Cross valid method: THROUGHOUT / ESU R: 0.148 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19136 7766 4.4 %RANDOM
Rwork0.16749 ---
obs0.16857 170141 99.91 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.947 Å2
Baniso -1Baniso -2Baniso -3
1-0.31 Å20.16 Å20 Å2
2--0.31 Å2-0 Å2
3----1.01 Å2
Refinement stepCycle: 1 / Resolution: 2.01→50.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15942 0 112 2001 18055
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.01216846
X-RAY DIFFRACTIONr_bond_other_d0.0010.01615216
X-RAY DIFFRACTIONr_angle_refined_deg1.0691.65222938
X-RAY DIFFRACTIONr_angle_other_deg0.3721.57435128
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.34552044
X-RAY DIFFRACTIONr_dihedral_angle_2_deg3.79.685254
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.0310.6862603
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.73515119
X-RAY DIFFRACTIONr_chiral_restr0.0530.22311
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_it2.3013.9698101
X-RAY DIFFRACTIONr_mcbond_other2.3013.9698101
X-RAY DIFFRACTIONr_mcangle_it3.3447.12410170
X-RAY DIFFRACTIONr_mcangle_other3.3467.12410171
X-RAY DIFFRACTIONr_scbond_it3.234.3398745
X-RAY DIFFRACTIONr_scbond_other3.234.3398746
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.1357.812769
X-RAY DIFFRACTIONr_long_range_B_refined7.14947.3119470
X-RAY DIFFRACTIONr_long_range_B_other7.13547.2319427
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
Rfree0.331 624 -
Rwork0.342 12296 -
obs--99.35 %

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