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Yorodumi- PDB-2p53: Crystal structure of N-acetyl-D-glucosamine-6-phosphate deacetyla... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2p53 | ||||||
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Title | Crystal structure of N-acetyl-D-glucosamine-6-phosphate deacetylase D273N mutant complexed with N-acetyl phosphonamidate-d-glucosamine-6-phosphate | ||||||
Components | N-acetylglucosamine-6-phosphate deacetylase | ||||||
Keywords | HYDROLASE / N-acetyl-D-glucosamine-6-phosphate deacetylase / aminohydrolase / (beta/alpha)8-barrel | ||||||
Function / homology | Function and homology information N-acetylglucosamine-6-phosphate deacetylase / N-acetylgalactosamine-6-phosphate deacetylase activity / N-acetylglucosamine-6-phosphate deacetylase activity / N-acetylglucosamine catabolic process / N-acetylneuraminate catabolic process / protein homotetramerization / protein-containing complex / zinc ion binding / identical protein binding Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Fedorov, A.A. / Fedorov, E.V. / Hall, R.S. / Raushel, F.M. / Almo, S.C. | ||||||
Citation | Journal: Biochemistry / Year: 2007 Title: Structural Diversity within the Mononuclear and Binuclear Active Sites of N-Acetyl-d-glucosamine-6-phosphate Deacetylase. Authors: Hall, R.S. / Brown, S. / Fedorov, A.A. / Fedorov, E.V. / Xu, C. / Babbitt, P.C. / Almo, S.C. / Raushel, F.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2p53.cif.gz | 160.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2p53.ent.gz | 125.9 KB | Display | PDB format |
PDBx/mmJSON format | 2p53.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p5/2p53 ftp://data.pdbj.org/pub/pdb/validation_reports/p5/2p53 | HTTPS FTP |
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-Related structure data
Related structure data | 2p50C 1ymyS 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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Details | The biological assembly is a dimer AB |
-Components
#1: Protein | Mass: 40990.961 Da / Num. of mol.: 2 / Mutation: D273N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: nagA, b0677, JW0663 / Production host: Escherichia coli (E. coli) References: UniProt: P0AF18, N-acetylglucosamine-6-phosphate deacetylase #2: Chemical | #3: Sugar | #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: 2.41 Å3/Da / Density % sol: 48.91 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 12% PEG 3350, 0.1M Hepes, 1mM Zn, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.98 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 15, 2006 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→25 Å / Num. all: 45044 / Num. obs: 45044 / % possible obs: 95.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Biso Wilson estimate: 18.8 Å2 / Rmerge(I) obs: 0.049 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1YMY Resolution: 2.1→24.85 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 138147.64 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0.1 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 54.2211 Å2 / ksol: 0.384019 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→24.85 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.18 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 10
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Xplor file |
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