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Yorodumi- PDB-1jt9: Structure of the mutant F174A T form of the Glucosamine-6-Phospha... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1jt9 | ||||||
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Title | Structure of the mutant F174A T form of the Glucosamine-6-Phosphate deaminase from E.coli | ||||||
Components | Glucosamine-6-Phosphate deaminase | ||||||
Keywords | HYDROLASE / ALLOSTERIC ENZYME / ENTROPIC EFFECTS / ALDOSE-KETOSE ISOMERASE / STRUCTURAL FLEXIBILITY | ||||||
Function / homology | Function and homology information glucosamine catabolic process / glucosamine-6-phosphate deaminase / glucosamine-6-phosphate deaminase activity / N-acetylglucosamine catabolic process / N-acetylneuraminate catabolic process / UDP-N-acetylglucosamine biosynthetic process / carbohydrate metabolic process / identical protein binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.06 Å | ||||||
Authors | Bustos-Jaimes, I. / Sosa-Peinado, A. / Rudino-Pinera, E. / Horjales, E. / Calcagno, M.L. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2002 Title: On the role of the conformational flexibility of the active-site lid on the allosteric kinetics of glucosamine-6-phosphate deaminase. Authors: Bustos-Jaimes, I. / Sosa-Peinado, A. / Rudino-Pinera, E. / Horjales, E. / Calcagno, M.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1jt9.cif.gz | 71.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jt9.ent.gz | 52.7 KB | Display | PDB format |
PDBx/mmJSON format | 1jt9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1jt9_validation.pdf.gz | 421.9 KB | Display | wwPDB validaton report |
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Full document | 1jt9_full_validation.pdf.gz | 427.9 KB | Display | |
Data in XML | 1jt9_validation.xml.gz | 15.3 KB | Display | |
Data in CIF | 1jt9_validation.cif.gz | 22.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jt/1jt9 ftp://data.pdbj.org/pub/pdb/validation_reports/jt/1jt9 | HTTPS FTP |
-Related structure data
Related structure data | 1cd5S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 29736.113 Da / Num. of mol.: 1 / Mutation: F174A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Species (production host): Escherichia coli / Production host: Escherichia coli K12 (bacteria) / Strain (production host): K12 References: UniProt: P0A759, glucosamine-6-phosphate deaminase |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: HEPES, sodium acetate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 18 ℃ | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 15, 2000 |
Radiation | Monochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 2.02→50 Å / % possible obs: 99 % / Redundancy: 3.4 % / Rsym value: 0.055 / Net I/σ(I): 11.1 |
Reflection shell | Resolution: 2.06→2.12 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 2.3 / Rsym value: 0.334 |
Reflection | *PLUS Lowest resolution: 50 Å / Num. obs: 41650 / % possible obs: 99 % / Rmerge(I) obs: 0.05 |
Reflection shell | *PLUS Rmerge(I) obs: 0.334 / Mean I/σ(I) obs: 11.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1cd5 Resolution: 2.06→47.13 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 36.1 Å2
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Refine analyze | Luzzati coordinate error obs: 0.24 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.19 Å | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.06→47.13 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.06→2.2 Å / Rfactor Rfree error: 0.01
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / Rfactor obs: 0.204 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 36.1 Å2 | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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