[English] 日本語
Yorodumi- PDB-3tny: Structure of YfiY from Bacillus cereus bound to the siderophore i... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3tny | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of YfiY from Bacillus cereus bound to the siderophore iron (III) schizokinen | ||||||
Components | YfiY (ABC transport system substrate-binding protein) | ||||||
Keywords | METAL TRANSPORT / schizokinen / bacillus cereus / nutrient binding protein / ABC transporter | ||||||
Function / homology | Nitrogenase molybdenum iron protein domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Chem-SKZ / : Function and homology information | ||||||
Biological species | Bacillus cereus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.55 Å | ||||||
Authors | Clifton, M.C. | ||||||
Citation | Journal: To be Published Title: Parsing the functional specificity of Siderocalin / Lipocalin 2 / NGAL for siderophores and related small-molecule ligands Authors: Clifton, M.C. / Rupert, P.B. / Hoette, T.M. / Raymond, K.N. / Abergel, R.J. / Strong, R.K. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3tny.cif.gz | 77.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3tny.ent.gz | 56.2 KB | Display | PDB format |
PDBx/mmJSON format | 3tny.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3tny_validation.pdf.gz | 900.3 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3tny_full_validation.pdf.gz | 901.8 KB | Display | |
Data in XML | 3tny_validation.xml.gz | 16.4 KB | Display | |
Data in CIF | 3tny_validation.cif.gz | 25.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tn/3tny ftp://data.pdbj.org/pub/pdb/validation_reports/tn/3tny | HTTPS FTP |
-Related structure data
Related structure data | 3cmpC 3hwdC 3hweC 3hwfC 3hwgC 3i0aC 3k3lC 3tf6C 3tzsC C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 34460.273 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus cereus (bacteria) / Gene: yfiY / Plasmid: pET101 / Production host: Escherichia coli (E. coli) / References: UniProt: C2Y5Z3 |
---|---|
#2: Chemical | ChemComp-SKZ / [ |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.69 Å3/Da / Density % sol: 54.2 % |
---|---|
Crystal grow | Temperature: 312 K / Method: vapor diffusion, hanging drop / pH: 7 Details: Protein 10-20 mg/ml, 0.1M HEPES 7.0, 30% Jeffamine ED-2001. Direct cryoprotection. , VAPOR DIFFUSION, HANGING DROP, temperature 312K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.97 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: May 1, 2010 |
Radiation | Monochromator: Liquid Nitrogen cooled Dual Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→50 Å / Num. obs: 46458 / % possible obs: 99.5 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.118 / Χ2: 0.949 / Net I/σ(I): 9.2 |
Reflection shell | Resolution: 1.55→1.61 Å / Χ2: 1.001 |
-Phasing
Phasing | Method: molecular replacement |
---|
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→50 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.961 / WRfactor Rfree: 0.2085 / WRfactor Rwork: 0.1868 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8909 / SU B: 1.21 / SU ML: 0.044 / SU R Cruickshank DPI: 0.0758 / SU Rfree: 0.0727 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.073 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 max: 56.47 Å2 / Biso mean: 21.1498 Å2 / Biso min: 12.36 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.55→50 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.55→1.59 Å / Total num. of bins used: 20
|