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- PDB-8fty: Crystal structure of the carotenoid isomerooxygenase, NinaB -

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Basic information

Entry
Database: PDB / ID: 8fty
TitleCrystal structure of the carotenoid isomerooxygenase, NinaB
Components(carotenoid isomerooxygenase) x 3
KeywordsOXIDOREDUCTASE / non-heme iron / isomerase / beta propeller / membrane / carotenoid
Function / homology
Function and homology information


beta-carotene 15,15'-dioxygenase activity / carotenoid dioxygenase activity / carotene catabolic process / retinal metabolic process / metal ion binding
Similarity search - Function
Carotenoid oxygenase / Retinal pigment epithelial membrane protein / Quinoprotein alcohol dehydrogenase-like superfamily
Similarity search - Domain/homology
CACODYLATE ION / : / Carotenoid isomerooxygenase
Similarity search - Component
Biological speciesTrichoplusia ni (cabbage looper)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsKiser, P.D. / Solano, Y.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE-2107713 United States
CitationJournal: Nat.Chem.Biol. / Year: 2024
Title: Carotenoid cleavage enzymes evolved convergently to generate the visual chromophore.
Authors: Solano, Y.J. / Everett, M.P. / Dang, K.S. / Abueg, J. / Kiser, P.D.
History
DepositionJan 14, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 17, 2024Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Derived calculations / Category: pdbx_struct_assembly / pdbx_struct_assembly_gen
Revision 1.2Feb 21, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Jun 12, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: carotenoid isomerooxygenase
B: carotenoid isomerooxygenase
C: carotenoid isomerooxygenase
D: carotenoid isomerooxygenase
E: carotenoid isomerooxygenase
F: carotenoid isomerooxygenase
G: carotenoid isomerooxygenase
H: carotenoid isomerooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)462,70536
Polymers460,2208
Non-polymers2,48628
Water37,3092071
1
A: carotenoid isomerooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,8435
Polymers57,5151
Non-polymers3284
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: carotenoid isomerooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,6893
Polymers57,5151
Non-polymers1742
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: carotenoid isomerooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,8084
Polymers57,5151
Non-polymers2923
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: carotenoid isomerooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,8666
Polymers57,5151
Non-polymers3515
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: carotenoid isomerooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,9776
Polymers57,5311
Non-polymers4465
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: carotenoid isomerooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,9615
Polymers57,5311
Non-polymers4294
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: carotenoid isomerooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,8404
Polymers57,5471
Non-polymers2923
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: carotenoid isomerooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,7213
Polymers57,5471
Non-polymers1742
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)349.934, 52.036, 210.036
Angle α, β, γ (deg.)90.00, 98.95, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-603-

CL

21D-604-

CL

31D-605-

NA

41A-823-

HOH

51A-850-

HOH

61A-878-

HOH

71D-2106-

HOH

81D-2272-

HOH

91D-2320-

HOH

101D-2332-

HOH

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Components

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Protein , 3 types, 8 molecules ABCDEFGH

#1: Protein
carotenoid isomerooxygenase


Mass: 57515.449 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trichoplusia ni (cabbage looper) / Gene: LOC113497779 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A7E5VY83
#2: Protein carotenoid isomerooxygenase


Mass: 57531.449 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trichoplusia ni (cabbage looper) / Gene: LOC113497779 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A7E5VY83
#3: Protein carotenoid isomerooxygenase


Mass: 57547.449 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trichoplusia ni (cabbage looper) / Gene: LOC113497779 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A7E5VY83

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Non-polymers , 6 types, 2099 molecules

#4: Chemical
ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C6H14O2 / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#8: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C2H6AsO2
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2071 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.11 Å3/Da / Density % sol: 41.79 % / Description: plates
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 40% (v/v) MPD 100 mM sodium cacodylate, pH 6.5 5% w/v PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 19, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 271195 / % possible obs: 98.6 % / Redundancy: 3.9 % / CC1/2: 0.996 / Rmerge(I) obs: 0.152 / Net I/σ(I): 5.6
Reflection shellResolution: 1.95→2.07 Å / Rmerge(I) obs: 1.401 / Mean I/σ(I) obs: 0.92 / Num. unique obs: 42167 / CC1/2: 0.435 / % possible all: 95.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0411refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→49.67 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.946 / SU B: 7.722 / SU ML: 0.192 / Cross valid method: THROUGHOUT / ESU R: 0.228 / ESU R Free: 0.178 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24677 13352 4.9 %RANDOM
Rwork0.21747 ---
obs0.21891 257803 98.56 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.073 Å2
Baniso -1Baniso -2Baniso -3
1--0.89 Å2-0 Å2-0.21 Å2
2--3.1 Å2-0 Å2
3----2.05 Å2
Refinement stepCycle: 1 / Resolution: 1.95→49.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms31357 0 137 2071 33565
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.01232601
X-RAY DIFFRACTIONr_bond_other_d0.0010.01630247
X-RAY DIFFRACTIONr_angle_refined_deg0.8441.65644398
X-RAY DIFFRACTIONr_angle_other_deg0.2961.57269737
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.04754008
X-RAY DIFFRACTIONr_dihedral_angle_2_deg0.74810382
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.46710.5365349
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.82415191
X-RAY DIFFRACTIONr_chiral_restr0.0420.24945
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0236853
X-RAY DIFFRACTIONr_gen_planes_other0.0010.027484
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_it1.5883.76315972
X-RAY DIFFRACTIONr_mcbond_other1.5873.76315972
X-RAY DIFFRACTIONr_mcangle_it2.626.75820000
X-RAY DIFFRACTIONr_mcangle_other2.626.75820001
X-RAY DIFFRACTIONr_scbond_it1.7173.97416629
X-RAY DIFFRACTIONr_scbond_other1.7173.97416630
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.8767.2224399
X-RAY DIFFRACTIONr_long_range_B_refined4.86346.9535904
X-RAY DIFFRACTIONr_long_range_B_other4.8646.9635880
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→1.999 Å
RfactorNum. reflection% reflection
Rfree0.433 942 -
Rwork0.426 17884 -
obs--92.89 %

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