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Yorodumi- PDB-2bkv: Structure and kinetics of a monomeric glucosamine-6-phosphate dea... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2bkv | ||||||
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Title | Structure and kinetics of a monomeric glucosamine-6-phosphate deaminase: missing link of the NagB superfamily | ||||||
Components | GLUCOSAMINE-6-PHOSPHATE DEAMINASE | ||||||
Keywords | HYDROLASE / SUBSTRATE INHIBITION / FRUCTOSE-6-PHOSPHATE | ||||||
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 / carbohydrate metabolic process / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | BACILLUS SUBTILIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Vincent, F. / Davies, G.J. / Brannigan, J.A. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2005 Title: Structure and Kinetics of a Monomeric Glucosamine 6-Phosphate Deaminase: Missing Link of the Nagb Superfamily Authors: Vincent, F. / Davies, G.J. / Brannigan, J.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2bkv.cif.gz | 212.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2bkv.ent.gz | 172.6 KB | Display | PDB format |
PDBx/mmJSON format | 2bkv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bk/2bkv ftp://data.pdbj.org/pub/pdb/validation_reports/bk/2bkv | HTTPS FTP |
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-Related structure data
Related structure data | 2bkxC 1deaS C: citing same article (ref.) 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: 27025.346 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) BACILLUS SUBTILIS (bacteria) / Strain: IG20 / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: O35000, glucosamine-6-phosphate deaminase #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: 1.9 Å3/Da / Density % sol: 36 % |
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-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9168 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9168 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→30 Å / Num. obs: 67231 / % possible obs: 98.8 % / Observed criterion σ(I): 2 / Redundancy: 5.6 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 14.6 |
Reflection shell | Resolution: 1.5→1.55 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 4.6 / % possible all: 97.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB EBTRY 1DEA Resolution: 1.5→72.55 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.931 / SU B: 2.646 / SU ML: 0.047 / Cross valid method: THROUGHOUT / ESU R: 0.104 / ESU R Free: 0.084 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 10.78 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→72.55 Å
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Refine LS restraints |
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