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Yorodumi- PDB-1p77: CRYSTAL STRUCTURE OF SHIKIMATE DEHYDROGENASE (AROE) FROM HAEMOPHI... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1p77 | |||||||||
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Title | CRYSTAL STRUCTURE OF SHIKIMATE DEHYDROGENASE (AROE) FROM HAEMOPHILUS INFLUENZAE | |||||||||
Components | Shikimate 5-dehydrogenase | |||||||||
Keywords | OXIDOREDUCTASE / Shikimate Dehydrogenase / Haemophilus influenzae / NADPH | |||||||||
Function / homology | Function and homology information shikimate dehydrogenase (NADP+) / shikimate metabolic process / shikimate 3-dehydrogenase (NADP+) activity / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / amino acid biosynthetic process / NADP binding / cytosol Similarity search - Function | |||||||||
Biological species | Haemophilus influenzae (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | |||||||||
Authors | Ye, S. / von Delft, F. / Brooun, A. / Knuth, M.W. / Swanson, R.V. / McRee, D.E. | |||||||||
Citation | Journal: J.Bacteriol. / Year: 2003 Title: The crystal structure of shikimate dehydrogenase (AroE) reveals a unique NADPH binding mode Authors: Ye, S. / von Delft, F. / Brooun, A. / Knuth, M.W. / Swanson, R.V. / McRee, D.E. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1p77.cif.gz | 72.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1p77.ent.gz | 52.2 KB | Display | PDB format |
PDBx/mmJSON format | 1p77.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1p77_validation.pdf.gz | 471.6 KB | Display | wwPDB validaton report |
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Full document | 1p77_full_validation.pdf.gz | 479.6 KB | Display | |
Data in XML | 1p77_validation.xml.gz | 8.5 KB | Display | |
Data in CIF | 1p77_validation.cif.gz | 13.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p7/1p77 ftp://data.pdbj.org/pub/pdb/validation_reports/p7/1p77 | HTTPS FTP |
-Related structure data
Related structure data | 1p74SC 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: 29788.002 Da / Num. of mol.: 1 / Fragment: Shikimate Dehydrogenase Source method: isolated from a genetically manipulated source Source: (gene. exp.) Haemophilus influenzae (bacteria) / Gene: AROE OR HI0655 / Plasmid: pSX12 / Production host: Escherichia coli (E. coli) / Strain (production host): DL41 References: UniProt: P43876, shikimate dehydrogenase (NADP+) |
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#2: Chemical | ChemComp-ACT / |
#3: Chemical | ChemComp-ATR / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.81 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.8 Details: 12% PEG 8000, 0.15 M Ca Acetate, 0.1 M Imidazole, pH 7.8, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K | ||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 8.8 / Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 200 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→50 Å / Num. all: 21069 / Num. obs: 21069 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.133 / Rsym value: 0.133 / Net I/σ(I): 9.8 |
Reflection shell | Resolution: 1.95→2.02 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.525 / Mean I/σ(I) obs: 2 / Num. unique all: 1908 / Rsym value: 0.525 / % possible all: 92 |
Reflection | *PLUS Num. measured all: 76173 |
Reflection shell | *PLUS % possible obs: 92 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1P74 Resolution: 1.95→20 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.898 / SU B: 4.505 / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.19 / ESU R Free: 0.167 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 10.429 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2.002 Å / 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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Software | *PLUS Version: 5 / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS % reflection Rfree: 5 % / Rfactor Rfree: 0.244 / Rfactor Rwork: 0.203 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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