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Yorodumi- PDB-1frz: GLUCOSAMINE-6-PHOSPHATE DEAMINASE FROM E.COLI, R CONFORMER. COMPL... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1frz | ||||||
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Title | GLUCOSAMINE-6-PHOSPHATE DEAMINASE FROM E.COLI, R CONFORMER. COMPLEXED WITH THE ALLOSTERIC ACTIVATOR N-ACETYL-GLUCOSAMINE-6-PHOSPHATE AT 2.2 A RESOLUTION | ||||||
Components | GLUCOSAMINE-6-PHOSPHATE DEAMINASE | ||||||
Keywords | ISOMERASE / ALLOSTERIC ENZYME / ENTROPIC EFFECTS / ALDOSE-KETOSE ISOMERASE | ||||||
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 / Resolution: 2.2 Å | ||||||
Authors | Rudino-Pinera, E. / Morales-Arrieta, S. / Rojas-Trejo, S.P. / Horjales, E. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2002 Title: Structural flexibility, an essential component of the allosteric activation in Escherichia coli glucosamine-6-phosphate deaminase. Authors: Rudino-Pinera, E. / Morales-Arrieta, S. / Rojas-Trejo, S.P. / Horjales, E. #1: Journal: Structure / Year: 1995 Title: Structure and catalytic mechanism of glucosamine-6-phosphate deaminase from Escherichia coli at 2.1A resolution Authors: Oliva, G. / Fontes, M.R.M. / Garratt, R.C. / Altamirano, M.M. / Calcagno, M.L. / Horjales, E. #2: Journal: Structure / Year: 1999 Title: The allosteric transition of glucosamine-6-phosphate deaminase: the structure of the T state at 2.3A resolution Authors: Horjales, E. / Altamirano, M.M. / Calcagno, M.L. / Garratt, R.C. / Oliva, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1frz.cif.gz | 119.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1frz.ent.gz | 94.2 KB | Display | PDB format |
PDBx/mmJSON format | 1frz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1frz_validation.pdf.gz | 491.7 KB | Display | wwPDB validaton report |
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Full document | 1frz_full_validation.pdf.gz | 504.4 KB | Display | |
Data in XML | 1frz_validation.xml.gz | 13.6 KB | Display | |
Data in CIF | 1frz_validation.cif.gz | 20.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fr/1frz ftp://data.pdbj.org/pub/pdb/validation_reports/fr/1frz | 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 on special symmetry positions |
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Details | The biological assembly is a hexamer constructed from monomers A and B generated by the three-fold |
-Components
#1: Protein | Mass: 29812.211 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: COMPLEXED WITH N-ACETYL-D-GLUCOSAMINE-6-PHOSPHATE / Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PTZ18-R / Production host: Escherichia coli (E. coli) / References: UniProt: P0A759, EC: 5.3.1.10 #2: Sugar | #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: 2.85 Å3/Da / Density % sol: 56.92 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: HEPES, sodium acetate, pH 7.5, VAPOR DIFFUSION, HANGING DROP at 291K | ||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion | ||||||||||||||||||||||||
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: 1.07 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 7, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.07 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. all: 30845 / % possible obs: 89.5 % / Observed criterion σ(F): 0 / Redundancy: 2.6 % / Biso Wilson estimate: 17.7 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 6.77 |
Reflection shell | Resolution: 2.2→2.34 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.305 / Num. unique all: 3846 / % possible all: 74.7 |
Reflection | *PLUS Highest resolution: 2.1 Å / Num. obs: 31426 / % possible obs: 90.5 % |
Reflection shell | *PLUS Highest resolution: 2.1 Å / Lowest resolution: 2.25 Å / % possible obs: 72.3 % / Mean I/σ(I) obs: 2.5 |
-Processing
Software |
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Refinement | Resolution: 2.2→50 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 63.2007 Å2 / ksol: 0.400966 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refine analyze | Luzzati coordinate error obs: 0.24 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.22 Å | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.34 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
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Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 50 Å / σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.199 / Rfactor Rfree: 0.228 | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.282 / % reflection Rfree: 10.2 % / Rfactor Rwork: 0.239 |