+Open data
-Basic information
Entry | Database: PDB / ID: 3f1l | ||||||
---|---|---|---|---|---|---|---|
Title | The 0.95 A structure of an oxidoreductase, yciK from E.coli | ||||||
Components | Uncharacterized oxidoreductase yciK | ||||||
Keywords | OXIDOREDUCTASE / yciK / E. coli / NADP+ | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Escherichia coli K12 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 0.95 Å | ||||||
Authors | Vijayalakshmi, J. / Woodard, R.W. | ||||||
Citation | Journal: to be published Title: Structure of an oxidoreductase, yciK from E. coli, in two crystal forms - NADP+ unbound structure at 0.95 A resolution Authors: Vijayalakshmi, J. / Meredith, T.C. / Woodard, R.W. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3f1l.cif.gz | 284.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3f1l.ent.gz | 235.9 KB | Display | PDB format |
PDBx/mmJSON format | 3f1l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3f1l_validation.pdf.gz | 445.5 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3f1l_full_validation.pdf.gz | 456.7 KB | Display | |
Data in XML | 3f1l_validation.xml.gz | 29.8 KB | Display | |
Data in CIF | 3f1l_validation.cif.gz | 45.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f1/3f1l ftp://data.pdbj.org/pub/pdb/validation_reports/f1/3f1l | HTTPS FTP |
-Related structure data
Related structure data | 3f1kSC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 27960.889 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K12 (bacteria) / Strain: K-12 MG1655 / Gene: b1271, JW1263, yciK / Plasmid: pT7-7 / Production host: Escherichia coli (E. coli) / References: UniProt: P31808, Oxidoreductases #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.98 Å3/Da / Density % sol: 37.84 % / Mosaicity: 1.932 ° |
---|---|
Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1M HEPES pH 7.5, 0.1M sodium nitrate, 16 % w/v polyethylene glycol 8000, vapor diffusion, hanging drop, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.9184 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MAR CCD 300 mm / Detector: CCD / Date: Apr 26, 2007 / Details: Si(III) Monochromator | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(III) Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 0.95→45.24 Å / Num. obs: 236813 / % possible obs: 86.7 % / Redundancy: 4.44 % / Biso Wilson estimate: 8.3 Å2 / Rmerge(I) obs: 0.062 / Χ2: 0.77 / Net I/σ(I): 8.9 / Scaling rejects: 29778 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
|
-Phasing
Phasing | Method: molecular replacement |
---|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3F1K, ycik structure at 2.6A resolution, solved by MAD and SAD phasing Resolution: 0.95→34.136 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.14 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 71.342 Å2 / ksol: 0.47 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 113.6 Å2 / Biso mean: 18.207 Å2 / Biso min: 0.09 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.95→34.136 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13
|