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Yorodumi- PDB-4db3: 1.95 Angstrom Resolution Crystal Structure of N-acetyl-D-glucosam... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4db3 | ||||||
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Title | 1.95 Angstrom Resolution Crystal Structure of N-acetyl-D-glucosamine kinase from Vibrio vulnificus. | ||||||
Components | N-acetyl-D-glucosamine kinase | ||||||
Keywords | TRANSFERASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID | ||||||
Function / homology | Function and homology information N-acetylglucosamine kinase / N-acetylglucosamine kinase activity / N-acetylglucosamine metabolic process / peptidoglycan turnover / zinc ion binding / ATP binding Similarity search - Function | ||||||
Biological species | Vibrio vulnificus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Minasov, G. / Wawrzak, Z. / Onopriyenko, O. / Skarina, T. / Papazisi, L. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Citation | Journal: TO BE PUBLISHED Title: 1.95 Angstrom Resolution Crystal Structure of N-acetyl-D-glucosamine kinase from Vibrio vulnificus. Authors: Minasov, G. / Wawrzak, Z. / Onopriyenko, O. / Skarina, T. / Papazisi, L. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4db3.cif.gz | 144.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4db3.ent.gz | 113.6 KB | Display | PDB format |
PDBx/mmJSON format | 4db3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/db/4db3 ftp://data.pdbj.org/pub/pdb/validation_reports/db/4db3 | HTTPS FTP |
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-Related structure data
Related structure data | 2ap1S S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 35352.152 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio vulnificus (bacteria) / Strain: CMCP6 / Gene: nagK, VV1_2570 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIPL / References: UniProt: Q8D9M7, N-acetylglucosamine kinase |
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-Non-polymers , 5 types, 198 molecules
#2: Chemical | ChemComp-ZN / | ||||||
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#3: Chemical | #4: Chemical | ChemComp-SO4 / | #5: Chemical | ChemComp-GOL / | #6: 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: 2.91 Å3/Da / Density % sol: 57.79 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7 Details: Protein solution: 2.5 mG/mL, 0.3M Sodium chloride, 0.01M HEPES pH 7.5. Screen solution: 0.1M Lithium sulfate, 0.1M Bis-Tris Propane pH 7.0. Cryo: 0.1M Li Sulfate, 0.1M Bis-Tris Propane, 20% ...Details: Protein solution: 2.5 mG/mL, 0.3M Sodium chloride, 0.01M HEPES pH 7.5. Screen solution: 0.1M Lithium sulfate, 0.1M Bis-Tris Propane pH 7.0. Cryo: 0.1M Li Sulfate, 0.1M Bis-Tris Propane, 20% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 15, 2011 / Details: Beryllium lenses |
Radiation | Monochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97856 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→30 Å / Num. all: 29453 / Num. obs: 29453 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Biso Wilson estimate: 32.7 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 23.1 |
Reflection shell | Resolution: 1.95→1.98 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.557 / Mean I/σ(I) obs: 2 / Num. unique all: 1434 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2AP1 Resolution: 1.95→29.45 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.962 / SU B: 7.262 / SU ML: 0.094 Isotropic thermal model: Thermal Factors Individually Refined Cross valid method: THROUGHOUT / ESU R: 0.129 / ESU R Free: 0.12 / 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: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.376 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→29.45 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2.001 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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