+Open data
-Basic information
Entry | Database: PDB / ID: 2uyp | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of E. coli TdcF with bound propionate | ||||||
Components | PROTEIN TDCF | ||||||
Keywords | UNKNOWN FUNCTION / YJGF/YER057C/UK114 FAMILY / 2-KETOBUTYRATE / PROPIONATE / TDCF PROTEIN / LIGAND BINDING | ||||||
Function / homology | Function and homology information L-threonine catabolic process to propionate / threonine metabolic process / organonitrogen compound catabolic process / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In cyclic amidines / deaminase activity / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | ESCHERICHIA COLI (E. coli) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.44 Å | ||||||
Authors | Burman, J.D. / Stevenson, C.E.M. / Sawers, R.G. / Lawson, D.M. | ||||||
Citation | Journal: Bmc Struct.Biol. / Year: 2007 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2uyp.cif.gz | 86.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2uyp.ent.gz | 65.7 KB | Display | PDB format |
PDBx/mmJSON format | 2uyp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uy/2uyp ftp://data.pdbj.org/pub/pdb/validation_reports/uy/2uyp | HTTPS FTP |
---|
-Related structure data
Related structure data | 2uyjC 2uykC 2uynC 1qu9S C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||||||
Unit cell |
| ||||||||||||||||
Components on special symmetry positions |
| ||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS oper:
|
-Components
#1: Protein | Mass: 14068.104 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: MC4100 / Plasmid: PETHF1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0AGL2 #2: Chemical | #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.02 Å3/Da / Density % sol: 46.49 % |
---|---|
Crystal grow | pH: 7 / Details: 10% PEG 1000, 8% PEG 8000, NO BUFFER, pH 7.00 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 11, 2002 / Details: OSMIC CONFOCAL MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→25.25 Å / Num. obs: 14818 / % possible obs: 98.9 % / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 35.93 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 12.49 |
Reflection shell | Resolution: 2.45→2.54 Å / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 2.58 / % possible all: 94 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1QU9 Resolution: 2.44→24.58 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.889 / SU B: 7.916 / SU ML: 0.187 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.541 / ESU R Free: 0.295 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.23 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.44→24.58 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|