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- PDB-6n1y: Structure of L509V CAO1 - growth condition 1 -

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Basic information

Entry
Database: PDB / ID: 6n1y
TitleStructure of L509V CAO1 - growth condition 1
ComponentsCarotenoid oxygenase
KeywordsOXIDOREDUCTASE / dioxygenase / non-heme iron protein / beta-propeller
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 / : / Carotenoid oxygenase
Function and homology information
Biological speciesNeurospora crassa (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.15 Å
AuthorsKhadka, N. / Kiser, P.D.
CitationJournal: J.Biol.Chem. / Year: 2019
Title: Evidence for distinct rate-limiting steps in the cleavage of alkenes by carotenoid cleavage dioxygenases.
Authors: Khadka, N. / Farquhar, E.R. / Hill, H.E. / Shi, W. / von Lintig, J. / Kiser, P.D.
History
DepositionNov 12, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jul 17, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
B: Carotenoid oxygenase
C: Carotenoid oxygenase
D: Carotenoid oxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)238,30112
Polymers237,9364
Non-polymers3658
Water13,151730
1
A: Carotenoid oxygenase
C: Carotenoid oxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,1506
Polymers118,9682
Non-polymers1834
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Carotenoid oxygenase
D: Carotenoid oxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,1506
Polymers118,9682
Non-polymers1834
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)101.210, 101.210, 450.180
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: 0 / Beg auth comp-ID: LEU / Beg label comp-ID: LEU / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 0 / 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 /


Mass: 59483.910 Da / Num. of mol.: 4 / Mutation: L509V
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-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 730 / 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: 2.8 Å3/Da / Density % sol: 56.03 %
Crystal growTemperature: 281.15 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 33% w/v sodium polyacrylate 0.1 M HEPES pH 6

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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: Jun 12, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 146769 / % possible obs: 99.9 % / Redundancy: 12.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.17 / Net I/σ(I): 10
Reflection shellResolution: 2.15→2.28 Å / Rmerge(I) obs: 2.535 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 23282 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0232refinement
XDSdata reduction
XDSdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5U8X

5u8x


Resolution: 2.15→49.37 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.953 / SU B: 6.438 / SU ML: 0.149 / Cross valid method: THROUGHOUT / ESU R: 0.206 / ESU R Free: 0.165 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21832 6490 4.4 %RANDOM
Rwork0.1979 ---
obs0.19884 140279 99.91 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å
Displacement parametersBiso mean: 52.532 Å2
Baniso -1Baniso -2Baniso -3
1-1.1 Å20.55 Å20 Å2
2--1.1 Å2-0 Å2
3----3.55 Å2
Refinement stepCycle: 1 / Resolution: 2.15→49.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15920 0 8 730 16658
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.01316472
X-RAY DIFFRACTIONr_bond_other_d0.0010.01714719
X-RAY DIFFRACTIONr_angle_refined_deg1.2271.65222402
X-RAY DIFFRACTIONr_angle_other_deg1.1151.57734165
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.52151994
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.73121.778956
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.452152551
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.26415119
X-RAY DIFFRACTIONr_chiral_restr0.0460.22001
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0218776
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023753
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_it2.4235.4767967
X-RAY DIFFRACTIONr_mcbond_other2.4235.4767966
X-RAY DIFFRACTIONr_mcangle_it3.6758.2089958
X-RAY DIFFRACTIONr_mcangle_other3.6768.2089959
X-RAY DIFFRACTIONr_scbond_it2.6845.7718505
X-RAY DIFFRACTIONr_scbond_other2.6835.7718505
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.3128.54512442
X-RAY DIFFRACTIONr_long_range_B_refined6.16261.65817652
X-RAY DIFFRACTIONr_long_range_B_other6.13261.57517539
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 / Rms dev position: 0.03 Å / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumber
11A16561
12B16561
21A16593
22C16593
31A16509
32D16509
41B16536
42C16536
51B16479
52D16479
61C16429
62D16429
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 368 -
Rwork0.364 10286 -
obs--99.34 %

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