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- PDB-5u90: Crystal structure of Co-CAO1 in complex with resveratrol -

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Basic information

Entry
Database: PDB / ID: 5u90
TitleCrystal structure of Co-CAO1 in complex with resveratrol
ComponentsCarotenoid oxygenase 1
KeywordsOXIDOREDUCTASE / carotenoid cleavage oxygenase beta propeller dioxygenase / carotenoid oxygenase
Function / homologycarotenoid dioxygenase activity / carotene catabolic process / Oxidoreductases; Acting on single donors with incorporation of molecular oxygen (oxygenases); With incorporation of two atoms of oxygen / Carotenoid oxygenase / Retinal pigment epithelial membrane protein / metal ion binding / : / RESVERATROL / Carotenoid cleavage oxygenase 1
Function and homology information
Biological speciesNeurospora crassa (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSui, X. / Palczewski, k. / Banerjee, S. / Kiser, P.D.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Eye Institute (NIH/NEI)EY009339 United States
National Institutes of Health/National Eye Institute (NIH/NEI)EY020551 United States
Burroughs Wellcome Fund1015187 United States
Dept of Veterans AffairsBX002683 United States
CitationJournal: Biochemistry / Year: 2017
Title: Structure and Spectroscopy of Alkene-Cleaving Dioxygenases Containing an Atypically Coordinated Non-Heme Iron Center.
Authors: Sui, X. / Weitz, A.C. / Farquhar, E.R. / Badiee, M. / Banerjee, S. / von Lintig, J. / Tochtrop, G.P. / Palczewski, K. / Hendrich, M.P. / Kiser, P.D.
History
DepositionDec 15, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 31, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 21, 2017Group: Database references / Structure summary / Category: citation / citation_author / struct_keywords
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name / _struct_keywords.text
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Carotenoid oxygenase 1
B: Carotenoid oxygenase 1
C: Carotenoid oxygenase 1
D: Carotenoid oxygenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)241,29128
Polymers237,9924
Non-polymers3,29924
Water27,7971543
1
A: Carotenoid oxygenase 1
D: Carotenoid oxygenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,10216
Polymers118,9962
Non-polymers2,10614
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Carotenoid oxygenase 1
C: Carotenoid oxygenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,18912
Polymers118,9962
Non-polymers1,19310
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)101.050, 101.050, 447.540
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: LEU / Beg label comp-ID: LEU / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEUAA30 - 52630 - 526
21LEULEUBB30 - 52630 - 526
12PROPROAA30 - 52530 - 525
22PROPROCC30 - 52530 - 525
13LEULEUAA30 - 52630 - 526
23LEULEUDD30 - 52630 - 526
14PROPROBB30 - 52530 - 525
24PROPROCC30 - 52530 - 525
15LEULEUBB30 - 52630 - 526
25LEULEUDD30 - 52630 - 526
16PROPROCC30 - 52530 - 525
26PROPRODD30 - 52530 - 525

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Carotenoid oxygenase 1


Mass: 59497.934 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987) (fungus)
Strain: ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987
Gene: cao-1, NCU07008 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7S860
#2: Chemical
ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Co
#3: Chemical
ChemComp-STL / RESVERATROL


Mass: 228.243 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C14H12O3
#4: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1543 / Source method: isolated from a natural source / Formula: H2O

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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: 2.77 Å3/Da / Density % sol: 55.62 %
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop / Details: sodium polyacrylate/HEPES 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97919 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97919 Å / Relative weight: 1
ReflectionResolution: 1.9→49.28 Å / Num. obs: 209824 / % possible obs: 100 % / Redundancy: 12.1 % / Net I/σ(I): 8.66

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5U8X

5u8x


Resolution: 1.9→49.28 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.966 / SU B: 4.435 / SU ML: 0.113 / Cross valid method: THROUGHOUT / ESU R: 0.121 / ESU R Free: 0.112 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19441 9432 4.5 %RANDOM
Rwork0.16812 ---
obs0.16934 200392 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 42.246 Å2
Baniso -1Baniso -2Baniso -3
1-0.39 Å20.2 Å20 Å2
2--0.39 Å20 Å2
3----1.27 Å2
Refinement stepCycle: 1 / Resolution: 1.9→49.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15958 0 214 1543 17715
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01916824
X-RAY DIFFRACTIONr_bond_other_d0.0020.0215330
X-RAY DIFFRACTIONr_angle_refined_deg1.5781.94122884
X-RAY DIFFRACTIONr_angle_other_deg0.9522.98935306
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.06952018
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.87123.592849
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.182152574
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.13115116
X-RAY DIFFRACTIONr_chiral_restr0.0980.22310
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0220225
X-RAY DIFFRACTIONr_gen_planes_other0.0020.024123
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_it2.8733.968049
X-RAY DIFFRACTIONr_mcbond_other2.8733.968050
X-RAY DIFFRACTIONr_mcangle_it3.6035.92310068
X-RAY DIFFRACTIONr_mcangle_other3.6035.92310069
X-RAY DIFFRACTIONr_scbond_it3.9234.3458775
X-RAY DIFFRACTIONr_scbond_other3.9234.3458775
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.5236.37612817
X-RAY DIFFRACTIONr_long_range_B_refined6.95446.72118851
X-RAY DIFFRACTIONr_long_range_B_other6.80746.17518427
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A334200.05
12B334200.05
21A333200.05
22C333200.05
31A334060.05
32D334060.05
41B333860.05
42C333860.05
51B335120.05
52D335120.05
61C335060.04
62D335060.04
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.442 626 -
Rwork0.447 14709 -
obs--99.95 %

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