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- PDB-4cnn: High resolution structure of Salmonella typhi type I dehydroquinase -
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Open data
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Basic information
Entry | Database: PDB / ID: 4cnn | ||||||
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Title | High resolution structure of Salmonella typhi type I dehydroquinase | ||||||
![]() | 3-DEHYDROQUINATE DEHYDRATASE | ||||||
![]() | LYASE / BACTERIAL PROTEINS / BINDING SITES / SHIKIMIS ACID PATHWAY | ||||||
Function / homology | ![]() 3,4-dihydroxybenzoate biosynthetic process / 3-dehydroquinate dehydratase / 3-dehydroquinate dehydratase activity / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / amino acid biosynthetic process Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Otero, J.M. / Llamas-Saiz, A.L. / Maneiro, M. / Peon, A. / Lence, E. / Lamb, H. / Hawkins, A.R. / Gonzalez-Bello, C. / van Raaij, M.J. | ||||||
![]() | ![]() Title: Mechanistic Insight Into the Reaction Catalyzed by Type I Dehydroquinase Authors: Maneiro, M. / Peon, A. / Lence, E. / Otero, J.M. / Llamas-Saiz, A. / van Raaij, M.J. / Lamb, H. / Hawkins, A.R. / Gonzalez-Bello, C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 243.3 KB | Display | ![]() |
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PDB format | ![]() | 196.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 457.1 KB | Display | ![]() |
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Full document | ![]() | 461.4 KB | Display | |
Data in XML | ![]() | 28.1 KB | Display | |
Data in CIF | ![]() | 44.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4cnpC ![]() 1qfeS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 27680.992 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() ![]() #2: Chemical | ChemComp-NA / #3: Chemical | #4: Chemical | ChemComp-CIT / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.3 % / Description: NONE |
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Crystal grow | pH: 6.4 / Details: 30% PEG 4000, 0.1 M CITRATE-PHOSPHATE PH 6.4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 8, 2013 / Details: PLANE-ELLIPSOIDAL MIRRORS (SI, RH, IR) |
Radiation | Monochromator: CHANNEL-CUT DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.09723 Å / Relative weight: 1 |
Reflection | Resolution: 1→84.36 Å / Num. obs: 190168 / % possible obs: 79.3 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 8.6 Å2 / Rmerge(I) obs: 0.03 / Net I/σ(I): 19.7 |
Reflection shell | Resolution: 1→1.05 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 2.3 / % possible all: 26.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1QFE Resolution: 1→51.2 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.975 / SU B: 0.636 / SU ML: 0.015 / Cross valid method: THROUGHOUT / ESU R: 0.027 / ESU R Free: 0.026 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES ARE REFINED INDIVIDUALLY. GAP BY DISORDERED REGION BETWEEN VAL-228 AND GLY-235 IN CHAIN A AND ALA-229 AND PRO-234 IN CHAIN B.
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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: 11.478 Å2
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Refinement step | Cycle: LAST / Resolution: 1→51.2 Å
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Refine LS restraints |
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