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- PDB-5dzs: 1.5 Angstrom Crystal Structure of Shikimate Dehydrogenase 1 from ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5dzs | ||||||
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Title | 1.5 Angstrom Crystal Structure of Shikimate Dehydrogenase 1 from Peptoclostridium difficile. | ||||||
![]() | Shikimate dehydrogenase (NADP(+)) | ||||||
![]() | OXIDOREDUCTASE / shikimate dehydrogenase 1 / CSGID / Structural genomics / Center for Structural Genomics of Infectious Diseases | ||||||
Function / homology | ![]() shikimate dehydrogenase (NADP+) / shikimate metabolic process / shikimate 3-dehydrogenase (NADP+) activity / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / amino acid biosynthetic process / NADP binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Minasov, G. / Wawrzak, Z. / Shuvalova, L. / Dubrovska, I. / Flores, K. / Grimshaw, S. / Kwon, K. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
![]() | ![]() Title: 1.5 Angstrom Crystal Structure of Shikimate Dehydrogenase 1 from Peptoclostridium difficile. Authors: Minasov, G. / Wawrzak, Z. / Shuvalova, L. / Dubrovska, I. / Flores, K. / Grimshaw, S. / Kwon, K. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 249 KB | Display | ![]() |
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PDB format | ![]() | 202.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 458.3 KB | Display | ![]() |
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Full document | ![]() | 465.6 KB | Display | |
Data in XML | ![]() | 26.1 KB | Display | |
Data in CIF | ![]() | 38.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3fbtS S: Starting model for refinement |
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Similar structure data | |
Other databases |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 31094.996 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: 630 / Gene: aroE1, CD630_18370 / Plasmid: pMCSG28 / Production host: ![]() ![]() References: UniProt: Q187E7, shikimate dehydrogenase (NADP+) #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44.4 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7 Details: Protein: 10.6 mg/ml, 0.01M Tris-HCL (pH 8.3); Screen: Classics II (F3), 0.064M Sodium citrate (pH 7.0), 0.1M HEPES (pH 7.0), 10% (w/v) PEG 5000 MME; Cryo: 1:1 (v/v), 50% Sucrose : screen solution. PH range: 7 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 22, 2015 |
Radiation | Monochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97856 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→30 Å / Num. obs: 82004 / % possible obs: 96.1 % / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Biso Wilson estimate: 23.6 Å2 / Rmerge(I) obs: 0.038 / Rsym value: 0.038 / Net I/σ(I): 29 |
Reflection shell | Resolution: 1.5→1.53 Å / Redundancy: 4 % / Rmerge(I) obs: 0.454 / Mean I/σ(I) obs: 3.1 / % possible all: 94.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3FBT Resolution: 1.5→29.7 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.966 / SU B: 2.641 / SU ML: 0.048 / Cross valid method: THROUGHOUT / ESU R: 0.075 / ESU R Free: 0.073 / 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: 38.531 Å2
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Refinement step | Cycle: 1 / Resolution: 1.5→29.7 Å
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Refine LS restraints |
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