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- PDB-5u8z: Structure of Fe-CAO1 in complex with beta-fluororesveratrol -

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Basic information

Entry
Database: PDB / ID: 5u8z
TitleStructure of Fe-CAO1 in complex with beta-fluororesveratrol
ComponentsCarotenoid oxygenase 1
KeywordsOXIDOREDUCTASE / carotenoid cleavage oxygenase beta propeller dioxygenase resveratrol / carotenoid oxygenase
Function / homologycarotenoid dioxygenase activity / carotene catabolic process / Carotenoid oxygenase / Retinal pigment epithelial membrane protein / Oxidoreductases; Acting on single donors with incorporation of molecular oxygen (oxygenases); With incorporation of two atoms of oxygen / metal ion binding / Chem-83D / : / 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. / Kiser, P.D.
Funding support United States, 6items
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
National Institutes of Health/National Cancer Institute (NIH/NCI)CA157735
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM77387
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 1.4Apr 13, 2022Group: Author supporting evidence / Database references / Derived calculations
Category: database_2 / pdbx_audit_support / struct_conn
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
Revision 1.5Oct 4, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_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)239,49818
Polymers237,9924
Non-polymers1,50614
Water28,6081588
1
A: Carotenoid oxygenase 1
D: Carotenoid oxygenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,82710
Polymers118,9962
Non-polymers8318
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)119,6718
Polymers118,9962
Non-polymers6756
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)101.037, 101.037, 448.622
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

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Protein , 1 types, 4 molecules ABCD

#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

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Non-polymers , 5 types, 1602 molecules

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


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#3: Chemical
ChemComp-83D / 5-[(Z)-2-fluoro-2-(4-hydroxyphenyl)ethenyl]benzene-1,3-diol


Mass: 246.234 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H11FO3
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1588 / 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: 2.78 Å3/Da / Density % sol: 55.72 %
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop / Details: Sodium polyacrylate/HEPES pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.9→49.28 Å / Num. obs: 205626 / % possible obs: 97.7 % / Redundancy: 9.7 % / Rmerge(I) obs: 0.17 / Net I/σ(I): 11.9
Reflection shellResolution: 1.9→2.01 Å / Redundancy: 8.8 % / Rmerge(I) obs: 2.1 / Mean I/σ(I) obs: 0.96 / % possible all: 88.5

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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: 0.967 / Cor.coef. Fo:Fc free: 0.953 / SU B: 4.338 / SU ML: 0.114 / Cross valid method: THROUGHOUT / ESU R: 0.133 / ESU R Free: 0.125 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21346 9497 4.6 %RANDOM
Rwork0.18168 ---
obs0.18318 196117 97.67 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å
Displacement parametersBiso mean: 35.403 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20.02 Å2-0 Å2
2--0.04 Å20 Å2
3----0.13 Å2
Refinement stepCycle: 1 / Resolution: 1.9→49.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15948 0 88 1588 17624
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01916610
X-RAY DIFFRACTIONr_bond_other_d0.0020.0215174
X-RAY DIFFRACTIONr_angle_refined_deg1.5491.94722596
X-RAY DIFFRACTIONr_angle_other_deg0.938334979
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.79352007
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.09123.579841
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.296152564
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.89415116
X-RAY DIFFRACTIONr_chiral_restr0.0940.22297
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02119392
X-RAY DIFFRACTIONr_gen_planes_other0.0020.024036
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_it2.6063.2828005
X-RAY DIFFRACTIONr_mcbond_other2.6033.2818003
X-RAY DIFFRACTIONr_mcangle_it3.554.90610008
X-RAY DIFFRACTIONr_mcangle_other3.5514.90610009
X-RAY DIFFRACTIONr_scbond_it3.3753.6538605
X-RAY DIFFRACTIONr_scbond_other3.3753.6538606
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.0925.34212586
X-RAY DIFFRACTIONr_long_range_B_refined6.6939.85118712
X-RAY DIFFRACTIONr_long_range_B_other6.6939.85518713
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded15.8554
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A330020.06
12B330020.06
21A331380.05
22C331380.05
31A331160.05
32D331160.05
41B329760.05
42C329760.05
51B331040.05
52D331040.05
61C331880.05
62D331880.05
LS refinement shellResolution: 1.899→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 617 -
Rwork0.366 11717 -
obs--80.15 %

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