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Open data
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Basic information
Entry | Database: PDB / ID: 2uyk | ||||||
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Title | Crystal structure of E. coli TdcF with bound serine | ||||||
![]() | PROTEIN TDCF | ||||||
![]() | UNKNOWN FUNCTION / YJGF/YER057C/UK114 FAMILY / ![]() ![]() ![]() | ||||||
Function / homology | ![]() L-threonine catabolic process to propionate / threonine metabolic process / ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Burman, J.D. / Stevenson, C.E.M. / Sawers, R.G. / Lawson, D.M. | ||||||
![]() | ![]() Title: The Crystal Structure of Escherichia Coli Tdcf, a Member of the Highly Conserved Yjgf/Yer057C/Uk114 Family. Authors: Burman, J.D. / Stevenson, C.E.M. / Sawers, R.G. / Lawson, D.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 169.2 KB | Display | ![]() |
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PDB format | ![]() | 135.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2uyjC ![]() 2uynC ![]() 2uypC ![]() 1qu9S 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 on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS oper:
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Components
#1: Protein | Mass: 14068.104 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-SER / | ![]() #3: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.02 Å3/Da / Density % sol: 46.99 % |
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Crystal grow![]() | pH: 7 / Details: 10% PEG 1000, 8% PEG 8000, NO BUFFER, pH 7.00 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Sep 28, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.6→35.53 Å / Num. obs: 50532 / % possible obs: 95.2 % / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Biso Wilson estimate: 15.8 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 15.82 |
Reflection shell | Resolution: 1.6→1.63 Å / Rmerge(I) obs: 0.12 / Mean I/σ(I) obs: 3.02 / % possible all: 66.4 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 1QU9 Resolution: 1.6→35.58 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.946 / SU B: 2.945 / SU ML: 0.048 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.111 / ESU R Free: 0.087 / 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 / VDW probe radii: 1.4 Å / Solvent model: MASK BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 11.32 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→35.58 Å
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Refine LS restraints |
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