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- PDB-3lta: Crystal structure of a non-biological ATP binding protein with a ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3lta | ||||||
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Title | Crystal structure of a non-biological ATP binding protein with a TYR-PHE mutation within the ligand binding domain | ||||||
![]() | ATP BINDING PROTEIN-DX | ||||||
![]() | 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'-TRIPHOSPHATE / DI(HYDROXYETHYL)ETHER![]() | ||||||
Biological species | synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Simmons, C.R. / Magee, C.L. / Allen, J.P. / Chaput, J.C. | ||||||
![]() | ![]() Title: Three-dimensional structures reveal multiple ADP/ATP binding modes for a synthetic class of artificial proteins. Authors: Simmons, C.R. / Magee, C.L. / Smith, D.A. / Lauman, L. / Chaput, J.C. / Allen, J.P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 30.6 KB | Display | ![]() |
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PDB format | ![]() | 19.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 814.4 KB | Display | ![]() |
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Full document | ![]() | 816.5 KB | Display | |
Data in XML | ![]() | 6 KB | Display | |
Data in CIF | ![]() | 7.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3lt8C ![]() 3lt9C ![]() 3ltbC ![]() 3ltcC ![]() 3ltdC ![]() 3g4b C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 9692.112 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) Description: THE PROTEIN IS A NON-BIOLOGICAL PROTEIN SELECTED FROM A RANDOM POOL OF PROTEIN SEQUENCES FOR THE ABILITY TO BIND ATP Plasmid: PIADL14 / Production host: ![]() ![]() |
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-Non-polymers , 5 types, 25 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/ATP.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ATP.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-ZN / | ||||
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#3: Chemical | ChemComp-ATP / | ||||
#4: Chemical | #5: Chemical | ChemComp-CL / | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.21 Å3/Da / Density % sol: 70.8 % |
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Crystal grow | pH: 8.5 Details: 0.1 M SODIUM PHOSPHATE PH 8.5, 0.25 M SODIUM CITRATE, 0.3 M SODIUM CHLORIDE, 23% PEG 400, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 18, 2008 |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.2817 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→50 Å / Num. obs: 4710 / % possible obs: 99.3 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.135 / Net I/σ(I): 15.385 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.57 / % possible all: 99.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3G4B ![]() 3g4b Resolution: 2.7→41.42 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.905 / SU B: 10.212 / SU ML: 0.197 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.328 / ESU R Free: 0.25 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES: REFINED INDIVIDUALLY
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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 mean: 32.69 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→41.42 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.77 Å / Total num. of bins used: 20
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