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- PDB-4k28: 2.15 Angstrom resolution crystal structure of a shikimate dehydro... -
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Open data
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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+ | |||||||||
![]() | Shikimate dehydrogenase family protein | |||||||||
![]() | OXIDOREDUCTASE / Rossmann-fold NAD(P)(+)-binding site / Shikimate dehydrogenase / NAD+ binding / Shikimate binding | |||||||||
Function / homology | ![]() | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Garcia, C. / Peek, J. / Petit, P. / Christendat, D. | |||||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 216.3 KB | Display | ![]() |
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PDB format | ![]() | 174.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 997.3 KB | Display | ![]() |
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Full document | ![]() | 1007.1 KB | Display | |
Data in XML | ![]() | 25 KB | Display | |
Data in CIF | ![]() | 34.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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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.) ![]() ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-MN / #4: Chemical | ChemComp-NA / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]()
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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 |