[English] 日本語
Yorodumi- PDB-3dgm: 2.4 A Structure of a Non-biological ATP binding protein with ADP bound -
+Open data
-Basic information
Entry | Database: PDB / ID: 3dgm | ||||||
---|---|---|---|---|---|---|---|
Title | 2.4 A Structure of a Non-biological ATP binding protein with ADP bound | ||||||
Components | ATP Binding Protein-DX | ||||||
Keywords | DE NOVO PROTEIN / alpha/beta fold / bent ATP / non-biological protein | ||||||
Function / homology | Nuclear Transport Factor 2; Chain: A, - #210 / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta / ADENOSINE-5'-DIPHOSPHATE / DI(HYDROXYETHYL)ETHER Function and homology information | ||||||
Biological species | unidentified (others) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Simmons, C.R. / Allen, J.P. / Chaput, J.C. | ||||||
Citation | Journal: To be Published Title: A Primordial ATP Binding Protein Generated from Random Sequence Origin Authors: Simmons, C.R. / Smith, D.A. / Watkins, J.L. / Stomel, J.M. / Allen, J.P. / Chaput, J.C. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3dgm.cif.gz | 31.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3dgm.ent.gz | 20.1 KB | Display | PDB format |
PDBx/mmJSON format | 3dgm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3dgm_validation.pdf.gz | 777.8 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3dgm_full_validation.pdf.gz | 778.2 KB | Display | |
Data in XML | 3dgm_validation.xml.gz | 6.8 KB | Display | |
Data in CIF | 3dgm_validation.cif.gz | 8.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dg/3dgm ftp://data.pdbj.org/pub/pdb/validation_reports/dg/3dgm | HTTPS FTP |
-Related structure data
Related structure data | |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 9708.112 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) unidentified (others) / Plasmid: pIADL14 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) |
---|---|
#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-ADP / |
#4: Chemical | ChemComp-PEG / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 4.48 Å3/Da / Density % sol: 72.54 % |
---|---|
Crystal grow | Temperature: 298 K / Method: sitting drop vapor diffusion / pH: 8.5 Details: 0.1 M sodium phosphate, 0.25 M sodium citrate, 0.3 M sodium chloride, 23% polyethylene glycol 400, 0.2 M ammonium acetate, pH 8.5, sitting drop vapor diffusion, temperature 298K |
-Data collection
Diffraction | Mean temperature: 143 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ROTATING ANODE / Wavelength: 1.5418 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Oct 23, 2007 / Details: 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: 2.4→30 Å / Num. obs: 6905 / % possible obs: 100 % / Redundancy: 9.5 % / Rmerge(I) obs: 0.164 / Χ2: 2.664 / Net I/σ(I): 7.9 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
|
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→27.44 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.937 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 4.678 / SU ML: 0.109 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.183 / ESU R Free: 0.16 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 500 Å2 / Biso mean: 26.824 Å2 / Biso min: 3.29 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→27.44 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.4→2.461 Å / Total num. of bins used: 20
|