+Open data
-Basic information
Entry | Database: PDB / ID: 6n1y | ||||||
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Title | Structure of L509V CAO1 - growth condition 1 | ||||||
Components | Carotenoid oxygenase | ||||||
Keywords | OXIDOREDUCTASE / dioxygenase / non-heme iron protein / beta-propeller | ||||||
Function / homology | Carotenoid 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 species | Neurospora crassa (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.15 Å | ||||||
Authors | Khadka, N. / Kiser, P.D. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6n1y.cif.gz | 412.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6n1y.ent.gz | 334 KB | Display | PDB format |
PDBx/mmJSON format | 6n1y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6n1y_validation.pdf.gz | 2.5 MB | Display | wwPDB validaton report |
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Full document | 6n1y_full_validation.pdf.gz | 2.5 MB | Display | |
Data in XML | 6n1y_validation.xml.gz | 72.2 KB | Display | |
Data in CIF | 6n1y_validation.cif.gz | 101.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n1/6n1y ftp://data.pdbj.org/pub/pdb/validation_reports/n1/6n1y | HTTPS FTP |
-Related structure data
Related structure data | 6n20C 6n21C 5u8xS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
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
NCS ensembles :
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-Components
#1: Protein | 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 / #3: Chemical | ChemComp-CL / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 56.03 % |
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Crystal grow | Temperature: 281.15 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 33% w/v sodium polyacrylate 0.1 M HEPES pH 6 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 12, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 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
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Solvent computation | Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 52.532 Å2
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Refinement step | Cycle: 1 / Resolution: 2.15→49.37 Å
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Refine LS restraints |
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