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Yorodumi- PDB-1doh: STRUCTURE OF TRIHYDROXYNAPHTHALENE REDUCTASE IN COMPLEX WITH NADP... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1doh | ||||||
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Title | STRUCTURE OF TRIHYDROXYNAPHTHALENE REDUCTASE IN COMPLEX WITH NADPH AND 4-NITRO-INDEN-1-ONE | ||||||
Components | TRIHYDROXYNAPHTHALENE REDUCTASE | ||||||
Keywords | OXIDOREDUCTASE / PROTEIN-NADPH-ACTIVE SITE INHIBITOR COMPLEX / DINUCLEOTIDE BINDING FOLD | ||||||
Function / homology | Function and homology information tetrahydroxynaphthalene reductase / tetrahydroxynaphthalene reductase activity / melanin biosynthetic process Similarity search - Function | ||||||
Biological species | Magnaporthe grisea (fungus) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.1 Å | ||||||
Authors | Liao, D.I. / Basarab, G.S. / Gatenby, A.A. / Jordan, D.B. | ||||||
Citation | Journal: Structure / Year: 2001 Title: Structures of trihydroxynaphthalene reductase-fungicide complexes: implications for structure-based design and catalysis. Authors: Liao, D. / Basarab, G.S. / Gatenby, A.A. / Valent, B. / Jordan, D.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1doh.cif.gz | 124.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1doh.ent.gz | 97.2 KB | Display | PDB format |
PDBx/mmJSON format | 1doh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1doh_validation.pdf.gz | 552.4 KB | Display | wwPDB validaton report |
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Full document | 1doh_full_validation.pdf.gz | 559.8 KB | Display | |
Data in XML | 1doh_validation.xml.gz | 13.7 KB | Display | |
Data in CIF | 1doh_validation.cif.gz | 22 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/do/1doh ftp://data.pdbj.org/pub/pdb/validation_reports/do/1doh | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 30177.682 Da / Num. of mol.: 2 / Mutation: S241V, A242Q, H247R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Magnaporthe grisea (fungus) / Plasmid: PTHNR2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) PET11 (NOVAGEN) References: UniProt: Q12634, tetrahydroxynaphthalene reductase #2: Chemical | #3: Chemical | #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: 3.56 Å3/Da / Density % sol: 65.41 % | ||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 Details: PEG6000, GLYCEROL, HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K | ||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ | ||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 18, 1997 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→30 Å / Num. all: 49907 / Num. obs: 47473 / % possible obs: 94.6 % / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Biso Wilson estimate: 25.47 Å2 / Rmerge(I) obs: 0.092 / Net I/σ(I): 14.9 |
Reflection shell | Resolution: 2.1→2.14 Å / Redundancy: 2.04 % / Rmerge(I) obs: 0.283 / % possible all: 76 |
Reflection | *PLUS Num. measured all: 209443 |
Reflection shell | *PLUS % possible obs: 76 % |
-Processing
Software |
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Refinement | Resolution: 2.1→8 Å / σ(F): 2
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Refinement step | Cycle: LAST / Resolution: 2.1→8 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.1 Å / Lowest resolution: 8 Å / σ(F): 2 / % reflection Rfree: 10 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |