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Yorodumi- PDB-4std: HIGH RESOLUTION STRUCTURES OF SCYTALONE DEHYDRATASE-INHIBITOR COM... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4std | ||||||
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Title | HIGH RESOLUTION STRUCTURES OF SCYTALONE DEHYDRATASE-INHIBITOR COMPLEXES CRYSTALLIZED AT PHYSIOLOGICAL PH | ||||||
Components | Scytalone dehydratase | ||||||
Keywords | LYASE | ||||||
Function / homology | Function and homology information scytalone dehydratase / scytalone dehydratase activity / melanin biosynthetic process / endosome / metal ion binding Similarity search - Function | ||||||
Biological species | Magnaporthe grisea (fungus) | ||||||
Method | X-RAY DIFFRACTION / MIR / Resolution: 2.15 Å | ||||||
Authors | Wawrzak, Z. / Sandalova, T. / Steffens, J.J. / Basarab, G.S. / Lundqvist, T. / Lindqvist, Y. / Jordan, D.B. | ||||||
Citation | Journal: Proteins / Year: 1999 Title: High-resolution structures of scytalone dehydratase-inhibitor complexes crystallized at physiological pH. Authors: Wawrzak, Z. / Sandalova, T. / Steffens, J.J. / Basarab, G.S. / Lundqvist, T. / Lindqvist, Y. / 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 | 4std.cif.gz | 116.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4std.ent.gz | 90.4 KB | Display | PDB format |
PDBx/mmJSON format | 4std.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4std_validation.pdf.gz | 519 KB | Display | wwPDB validaton report |
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Full document | 4std_full_validation.pdf.gz | 526.2 KB | Display | |
Data in XML | 4std_validation.xml.gz | 12.2 KB | Display | |
Data in CIF | 4std_validation.cif.gz | 18.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/st/4std ftp://data.pdbj.org/pub/pdb/validation_reports/st/4std | HTTPS FTP |
-Related structure data
Related structure data | 5stdC 6stdC 7stdC 1stdS 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: 19375.893 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Magnaporthe grisea (fungus) / Production host: Escherichia coli (E. coli) / References: UniProt: P56221, scytalone dehydratase #2: Chemical | #3: 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: 2.48 Å3/Da / Density % sol: 50.4 % | ||||||||||||||||||
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Crystal grow | pH: 7.5 / Details: pH 7.5 | ||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→20.11 Å / Num. obs: 31905 / % possible obs: 98.3 % / Observed criterion σ(I): 2 / Redundancy: 2.5 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 18.7 |
Reflection shell | Highest resolution: 2.15 Å / % possible all: 96.9 |
Reflection | *PLUS Num. measured all: 427017 |
Reflection shell | *PLUS % possible obs: 96.9 % |
-Processing
Software |
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Refinement | Method to determine structure: MIR Starting model: 1STD Resolution: 2.15→8 Å / σ(F): 2
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Displacement parameters | Biso mean: 15.8 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.15→8 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 8 Å / σ(F): 2 / % reflection Rfree: 7.5 % / Rfactor obs: 0.224 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 15.8 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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