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Open data
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Basic information
Entry | Database: PDB / ID: 6jw6 | ||||||
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Title | The crystal structure of KanD2 in complex with NAD | ||||||
![]() | Dehydrogenase | ||||||
![]() | OXIDOREDUCTASE / Rossmann fold / NAD binding | ||||||
Function / homology | Gfo/Idh/MocA-like oxidoreductase, C-terminal / Oxidoreductase family, C-terminal alpha/beta domain / Gfo/Idh/MocA-like oxidoreductase, N-terminal / Oxidoreductase family, NAD-binding Rossmann fold / NAD(P)-binding domain superfamily / nucleotide binding / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Dehydrogenase![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kudo, F. / Kitayama, Y. / Miyanaga, A. / Hirayama, A. / Eguchi, T. | ||||||
![]() | ![]() Title: Biochemical and structural analysis of a dehydrogenase, KanD2, and an aminotransferase, KanS2, that are responsible for the construction of the kanosamine moiety in kanamycin biosynthesis. Authors: Kudo, F. / Kitayama, Y. / Miyanaga, A. / Hirayama, A. / Eguchi, T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 275.9 KB | Display | ![]() |
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PDB format | ![]() | 224.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1014 KB | Display | ![]() |
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Full document | ![]() | 1021.8 KB | Display | |
Data in XML | ![]() | 25.9 KB | Display | |
Data in CIF | ![]() | 34.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6jw7C ![]() 6jw8C ![]() 4h3vS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: VAL / End label comp-ID: VAL / Refine code: _ / Auth seq-ID: 4 - 361 / Label seq-ID: 4 - 361
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Components
#1: Protein | Mass: 41108.059 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q6L737, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.39 Å3/Da / Density % sol: 63.73 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: PEG 8000, imidazole, calcium acetate, NAD |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 21, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. obs: 27212 / % possible obs: 100 % / Redundancy: 11.1 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 23.3 |
Reflection shell | Resolution: 2.8→2.95 Å / Redundancy: 11.3 % / Rmerge(I) obs: 0.918 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 3916 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4H3V Resolution: 2.8→48.18 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.929 / SU B: 26.569 / SU ML: 0.231 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.595 / ESU R Free: 0.315 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 176.51 Å2 / Biso mean: 79.263 Å2 / Biso min: 44.62 Å2
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Refinement step | Cycle: final / Resolution: 2.8→48.18 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 20175 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05
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LS refinement shell | Resolution: 2.8→2.873 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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