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Yorodumi- PDB-4k28: 2.15 Angstrom resolution crystal structure of a shikimate dehydro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4k28 | |||||||||
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Title | 2.15 Angstrom resolution crystal structure of a shikimate dehydrogenase family protein from Pseudomonas putida KT2440 in complex with NAD+ | |||||||||
Components | Shikimate dehydrogenase family protein | |||||||||
Keywords | OXIDOREDUCTASE / Rossmann-fold NAD(P)(+)-binding site / Shikimate dehydrogenase / NAD+ binding / Shikimate binding | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Pseudomonas putida (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.15 Å | |||||||||
Authors | Garcia, C. / Peek, J. / Petit, P. / Christendat, D. | |||||||||
Citation | Journal: Biochim.Biophys.Acta / Year: 2013 Title: Insights into the function of RifI2: structural and biochemical investigation of a new shikimate dehydrogenase family protein. Authors: Peek, J. / Garcia, C. / Lee, J. / Christendat, D. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4k28.cif.gz | 216.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4k28.ent.gz | 174.4 KB | Display | PDB format |
PDBx/mmJSON format | 4k28.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k2/4k28 ftp://data.pdbj.org/pub/pdb/validation_reports/k2/4k28 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 28096.125 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas putida (bacteria) / Strain: KT2440 / Gene: pp2608, PP_2608 / Plasmid: p15TV-L / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q88JP1 #2: Chemical | #3: Chemical | ChemComp-MN / #4: Chemical | ChemComp-NA / | #5: 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: 2.32 Å3/Da / Density % sol: 47.09 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.1 Details: 0.1M sodium citrate, 0.2M ammonium acetate, 20% PEG 8000 , pH 5.1, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54178 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 18, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→19.22 Å / Num. all: 29340 / Num. obs: 29145 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 5.8 % / Biso Wilson estimate: 30.9 Å2 / Rmerge(I) obs: 0.091 / Rsym value: 0.083 / Net I/σ(I): 17.5 |
Reflection shell | Resolution: 2.15→2.27 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.626 / Mean I/σ(I) obs: 3.2 / Num. unique all: 4202 / Rsym value: 0.559 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→19.22 Å / SU ML: 0.3 / σ(F): 0.02 / Phase error: 22.62 / 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 / Bsol: 33.413 Å2 / ksol: 0.329 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.15→19.22 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -13.9082 Å / Origin y: 13.7382 Å / Origin z: -18.9135 Å
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Refinement TLS group | Selection details: all |