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Yorodumi- PDB-4q6t: The crystal structure of a class V chitininase from Pseudomonas f... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4q6t | ||||||
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Title | The crystal structure of a class V chitininase from Pseudomonas fluorescens Pf-5 | ||||||
Components | Glycosyl hydrolase, family 18Glycoside hydrolase | ||||||
Keywords | HYDROLASE / structural genomics / PSI-Biology / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Pseudomonas protegens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.4 Å | ||||||
Authors | Tan, K. / Mack, J.C. / Endres, M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: The crystal structure of a class V chitininase from Pseudomonas fluorescens Pf-5 Authors: Tan, K. / Mack, J.C. / Endres, M. / Joachimiak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4q6t.cif.gz | 155.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4q6t.ent.gz | 127.9 KB | Display | PDB format |
PDBx/mmJSON format | 4q6t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q6/4q6t ftp://data.pdbj.org/pub/pdb/validation_reports/q6/4q6t | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 38244.176 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas protegens (bacteria) / Strain: Pf-5 / Gene: PFL_1213 / Plasmid: pMCSG68 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) pGrow7-K / References: UniProt: Q4KHD9 |
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-Non-polymers , 5 types, 392 molecules
#2: Chemical | #3: Chemical | ChemComp-GOL / | #4: Chemical | ChemComp-CL / | #5: Chemical | ChemComp-CD / | #6: 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: 2.16 Å3/Da / Density % sol: 43.05 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.005 M Cobalt Chloride, 0.005 M Magnesium Chloride, 0.005 M Cadmium Chloride, 0.005 M Nickel Chloride, 0.1 M HEPES:NaOH, 12% (w/v) PEG 3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 297K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97915 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 13, 2013 / Details: mirror |
Radiation | Monochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→25.5 Å / Num. all: 65837 / Num. obs: 65837 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -5 / Redundancy: 7.1 % / Biso Wilson estimate: 14.05 Å2 / Rmerge(I) obs: 0.092 / Net I/σ(I): 40 |
Reflection shell | Resolution: 1.4→1.42 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.714 / Mean I/σ(I) obs: 2.81 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.4→25.458 Å / SU ML: 0.12 / σ(F): 1.34 / Phase error: 15.06 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.4→25.458 Å
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Refine LS restraints |
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LS refinement shell |
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