+Open data
-Basic information
Entry | Database: PDB / ID: 6c3c | |||||||||
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Title | PLP-dependent L-arginine hydroxylase RohP quinonoid I complex | |||||||||
Components | Uncharacterized protein | |||||||||
Keywords | BIOSYNTHETIC PROTEIN / O2- / PLP-dependent hydroxylase | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Streptomyces cattleya (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | |||||||||
Authors | Hedges, J.B. / Ryan, K.S. | |||||||||
Funding support | Canada, United States, 2items
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Citation | Journal: ACS Chem. Biol. / Year: 2018 Title: Snapshots of the Catalytic Cycle of an O2, Pyridoxal Phosphate-Dependent Hydroxylase. Authors: Hedges, J.B. / Kuatsjah, E. / Du, Y.L. / Eltis, L.D. / Ryan, K.S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6c3c.cif.gz | 189.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6c3c.ent.gz | 146.3 KB | Display | PDB format |
PDBx/mmJSON format | 6c3c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c3/6c3c ftp://data.pdbj.org/pub/pdb/validation_reports/c3/6c3c | HTTPS FTP |
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-Related structure data
Related structure data | 6c3aC 6c3bC 6c3dC 5dj1S 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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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 47283.688 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces cattleya (bacteria) Strain: ATCC 35852 / DSM 46488 / JCM 4925 / NBRC 14057 / NRRL 8057 Gene: SCATT_03970 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G8WNK6*PLUS #2: Chemical | ChemComp-EDO / #3: Chemical | #4: Chemical | #5: 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: 2.38 Å3/Da / Density % sol: 48.35 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.2 M sodium malonate pH 7, 16-20% (w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å | |||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 19, 2017 | |||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.5→56.62 Å / Num. obs: 141151 / % possible obs: 100 % / Redundancy: 6.2 % / Biso Wilson estimate: 13.26 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.041 / Rrim(I) all: 0.103 / Net I/σ(I): 10.8 | |||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5DJ1 Resolution: 1.5→56.617 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.26
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 65.45 Å2 / Biso mean: 18.3686 Å2 / Biso min: 6.4 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.5→56.617 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30 / % reflection obs: 100 %
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