[English] 日本語
Yorodumi- PDB-6f2m: Structure of the bacteriophage T5 distal tail protein pb9 co-crys... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6f2m | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of the bacteriophage T5 distal tail protein pb9 co-crystallized with 10mM Tb-Xo4 | ||||||
Components | Distal tail protein | ||||||
Keywords | VIRAL PROTEIN / phage protein / Crystallophore / Tb-Xo4 / nucleation / phasing / lanthanide complexes | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Escherichia phage T5 (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å | ||||||
Authors | Engilberge, S. / Riobe, F. / Di Pietro, S. / Breyton, C. / Girard, E. / Dumont, E. / Maury, O. | ||||||
Funding support | France, 1items
| ||||||
Citation | Journal: Chemistry / Year: 2018 Title: Unveiling the Binding Modes of the Crystallophore, a Terbium-based Nucleating and Phasing Molecular Agent for Protein Crystallography. Authors: Engilberge, S. / Riobe, F. / Wagner, T. / Di Pietro, S. / Breyton, C. / Franzetti, B. / Shima, S. / Girard, E. / Dumont, E. / Maury, O. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6f2m.cif.gz | 569.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6f2m.ent.gz | 489.9 KB | Display | PDB format |
PDBx/mmJSON format | 6f2m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f2/6f2m ftp://data.pdbj.org/pub/pdb/validation_reports/f2/6f2m | HTTPS FTP |
---|
-Related structure data
Related structure data | 6f2fC 6f2hC 6f2iC 6f2jC 6f2kC 6frmC 6frnC 6froC 6frqC C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
4 |
| ||||||||
Unit cell |
|
-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 24479.426 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia phage T5 (virus) / Gene: D16, ORF128, T5.139, T5p135 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6QGE8 |
---|
-Non-polymers , 6 types, 665 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-CL / | #5: Chemical | ChemComp-NA / | #6: Chemical | #7: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.28 % / Description: Crystals look like square plates |
---|---|
Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop Details: 100mM HEPES pH 7.5 / 8% Ethylene glycol / 6% - 16% PEG8000. Tb-Xo4 was directly mixed with the protein solution at a final concentration of 10 mM prior to crystallization. |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.63137 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 7, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.63137 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→48.16 Å / Num. obs: 83616 / % possible obs: 96.58 % / Redundancy: 6.6 % / Biso Wilson estimate: 31.09 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.036 / Net I/σ(I): 13.11 |
Reflection shell | Resolution: 1.8→1.9 Å |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SAD / Resolution: 1.8→48.16 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.937 / SU R Cruickshank DPI: 0.14 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.112 / SU Rfree Blow DPI: 0.105 / SU Rfree Cruickshank DPI: 0.103
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.64 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.23 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.8→48.16 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.8→1.85 Å / Total num. of bins used: 20
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|