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Yorodumi- PDB-3ltd: X-ray structure of a non-biological ATP binding protein determine... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ltd | ||||||
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Title | X-ray structure of a non-biological ATP binding protein determined at 2.8 A by multi-wavelength anomalous dispersion | ||||||
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 | synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.8 Å | ||||||
Authors | Simmons, C.R. / Magee, C.L. / Allen, J.P. / Chaput, J.C. | ||||||
Citation | Journal: Biochemistry / Year: 2010 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ltd.cif.gz | 29.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ltd.ent.gz | 18.7 KB | Display | PDB format |
PDBx/mmJSON format | 3ltd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ltd_validation.pdf.gz | 756 KB | Display | wwPDB validaton report |
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Full document | 3ltd_full_validation.pdf.gz | 756.2 KB | Display | |
Data in XML | 3ltd_validation.xml.gz | 5.5 KB | Display | |
Data in CIF | 3ltd_validation.cif.gz | 6.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lt/3ltd ftp://data.pdbj.org/pub/pdb/validation_reports/lt/3ltd | HTTPS FTP |
-Related structure data
-Links
-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: 9708.112 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) Description: THE CONSTRUCT IS A NON-BIOLOGICAL ATP BINDING PROTEIN THAT WAS DISCOVERED THROUGH DIRECTED EVOLUTION. Plasmid: PIADL14 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) |
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-Non-polymers , 5 types, 20 molecules
#2: Chemical | #3: Chemical | ChemComp-ZN / | #4: Chemical | ChemComp-ADP / | #5: Chemical | ChemComp-CL / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.36 Å3/Da / Density % sol: 71.78 % Description: The Structure Factor File contains Friedel pairs |
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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: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 1.2817, 1.2750, 1.2822 | ||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 18, 2008 | ||||||||||||
Radiation | Monochromator: SI(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.8→50 Å / Num. obs: 4054 / % possible obs: 92.5 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.148 / Net I/σ(I): 12.69 | ||||||||||||
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.505 / % possible all: 94.3 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.8→36.56 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.904 / SU B: 9.14 / SU ML: 0.176 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.369 / ESU R Free: 0.259 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: THE FRIEDEL PAIRS WERE USED IN PHASING. 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: 26.57 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→36.56 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.87 Å / Total num. of bins used: 20
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