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- PDB-6b86: 2.2A Crystal Structure of Co-CAO1 -

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Basic information

Entry
Database: PDB / ID: 6b86
Title2.2A Crystal Structure of Co-CAO1
ComponentsCarotenoid oxygenase 1
KeywordsOXIDOREDUCTASE / beta-propeller / dioxygenase
Function / homologycarotenoid dioxygenase activity / 9-cis-epoxycarotenoid 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 / : / Carotenoid cleavage oxygenase 1
Function and homology information
Biological speciesNeurospora crassa (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.2 Å
AuthorsHill, H.E. / Kiser, P.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Eye Institute (NIH/NEI)EY009339 United States
CitationJournal: J. Biol. Inorg. Chem. / Year: 2018
Title: Preparation and characterization of metal-substituted carotenoid cleavage oxygenases.
Authors: Sui, X. / Farquhar, E.R. / Hill, H.E. / von Lintig, J. / Shi, W. / Kiser, P.D.
History
DepositionOct 5, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 4, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 16, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _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
Revision 1.2Feb 20, 2019Group: Author supporting evidence / Data collection / 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)238,2278
Polymers237,9924
Non-polymers2364
Water17,204955
1
A: Carotenoid oxygenase 1
D: Carotenoid oxygenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,1144
Polymers118,9962
Non-polymers1182
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)119,1144
Polymers118,9962
Non-polymers1182
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7520 Å2
ΔGint-43 kcal/mol
Surface area71210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.695, 100.695, 448.380
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 / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _ / Auth seq-ID: 30 - 526 / Label seq-ID: 30 - 526

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14BB
24CC
15BB
25DD
16CC
26DD

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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 955 / 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: 2.76 Å3/Da / Density % sol: 55.39 %
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop / Details: 50mM HEPES pH 6.5, 39% sodium polyacrylate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 133339 / % possible obs: 98 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 10.43
Reflection shellResolution: 2.2→2.3 Å / Rmerge(I) obs: 1.089 / Num. unique all: 20826 / % possible all: 96.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
XDSdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5U8Y

5u8y


Resolution: 2.2→49.12 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.96 / SU B: 7.493 / SU ML: 0.164 / Cross valid method: THROUGHOUT / ESU R: 0.213 / ESU R Free: 0.168 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20529 6067 4.6 %RANDOM
Rwork0.17878 ---
obs0.18002 127272 98.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 52.503 Å2
Baniso -1Baniso -2Baniso -3
1-0.74 Å20.37 Å2-0 Å2
2--0.74 Å20 Å2
3----2.41 Å2
Refinement stepCycle: 1 / Resolution: 2.2→49.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15924 0 4 955 16883
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01916420
X-RAY DIFFRACTIONr_bond_other_d0.0020.0214676
X-RAY DIFFRACTIONr_angle_refined_deg1.3591.9522324
X-RAY DIFFRACTIONr_angle_other_deg0.916334068
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.69251984
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.08123.51832
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.29152544
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.23215116
X-RAY DIFFRACTIONr_chiral_restr0.0810.22280
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02118556
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023608
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_it2.7135.1347948
X-RAY DIFFRACTIONr_mcbond_other2.7135.1337947
X-RAY DIFFRACTIONr_mcangle_it4.0267.6959928
X-RAY DIFFRACTIONr_mcangle_other4.0267.6959929
X-RAY DIFFRACTIONr_scbond_it3.1445.4638472
X-RAY DIFFRACTIONr_scbond_other3.1445.4638472
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.9628.06712396
X-RAY DIFFRACTIONr_long_range_B_refined7.37558.46717651
X-RAY DIFFRACTIONr_long_range_B_other7.35358.27617458
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)
11A324380.05
12B324380.05
21A324240.06
22C324240.06
31A324940.06
32D324940.06
41B325180.05
42C325180.05
51B325680.05
52D325680.05
61C327280.04
62D327280.04
LS refinement shellResolution: 2.197→2.253 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.357 261 -
Rwork0.356 8979 -
obs--93.37 %

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