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Yorodumi- PDB-1uw1: A Novel ADP- and Zinc-binding fold from function-directed in vitr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1uw1 | ||||||
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Title | A Novel ADP- and Zinc-binding fold from function-directed in vitro evolution | ||||||
Components | ARTIFICIAL NUCLEOTIDE BINDING PROTEIN (ANBP) | ||||||
Keywords | DE NOVO PROTEIN / ARTIFICIAL NUCLEOTIDE BINDING PROTEIN / NUCLEOTIDE BINDING PROTEIN / IN VITRO EVOLUTION | ||||||
Function / homology | Nuclear Transport Factor 2; Chain: A, - #210 / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta / ADENOSINE-5'-DIPHOSPHATE Function and homology information | ||||||
Biological species | SYNTHETIC CONSTRUCT (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.94 Å | ||||||
Authors | Lo Surdo, P. / Walsh, M.A. / Sollazzo, M. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2004 Title: A Novel Adp- and Zinc-Binding Fold from Function-Directed in Vitro Evolution Authors: Lo Surdo, P. / Walsh, M.A. / Sollazzo, M. #1: Journal: Nature / Year: 2001 Title: Functional Proteins from a Random Sequence Library Authors: Keefe, A.D. / Szostak, J.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1uw1.cif.gz | 32.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1uw1.ent.gz | 21.3 KB | Display | PDB format |
PDBx/mmJSON format | 1uw1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1uw1_validation.pdf.gz | 788.2 KB | Display | wwPDB validaton report |
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Full document | 1uw1_full_validation.pdf.gz | 788.2 KB | Display | |
Data in XML | 1uw1_validation.xml.gz | 6.8 KB | Display | |
Data in CIF | 1uw1_validation.cif.gz | 8.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uw/1uw1 ftp://data.pdbj.org/pub/pdb/validation_reports/uw/1uw1 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 9605.979 Da / Num. of mol.: 1 / Fragment: NUCLEOTIDE BINDING DOMAIN Source method: isolated from a genetically manipulated source Details: THIS IS A RANDOMLY GENERATED PROTEIN. THE PROTEIN WAS ISOLATED BY CYCLES OF IN VITRO EVOLUTIONARY SELECTION, FROM A RANDOM-SEQUENCE LIBRARY OF 6 X 10**12 MRNA-DISPLAYED PROTEINS. EVOLUTION ...Details: THIS IS A RANDOMLY GENERATED PROTEIN. THE PROTEIN WAS ISOLATED BY CYCLES OF IN VITRO EVOLUTIONARY SELECTION, FROM A RANDOM-SEQUENCE LIBRARY OF 6 X 10**12 MRNA-DISPLAYED PROTEINS. EVOLUTION OF THE PROTEINS PRODUCED WAS DIRECTED BY THE ABILITY TO BIND ATP Source: (gene. exp.) SYNTHETIC CONSTRUCT (others) / Description: SYNTHETIC GENE / Plasmid: MODIFIED PET-24D WITH N-HIS-TEV CLEAVAGE SITE / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) |
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#2: Chemical | ChemComp-ADP / |
#3: Chemical | ChemComp-ZN / |
#4: Water | ChemComp-HOH / |
Compound details | THE ORIGINAL FUNCTIONAL PROTEIN ISOLATED BY KEEFE AND SZOSTAK (NCBI: AAK50879, GI:13958624) ...THE ORIGINAL FUNCTIONAL |
Sequence details | THE ORIGINAL FUNCTIONAL PROTEIN ISOLATED BY KEEFE AND SZOSTAK (NCBI: AAK50879, GI:13958624) ...THE ORIGINAL FUNCTIONAL |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.4 Å3/Da / Density % sol: 72.1 % | |||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 7.5 Details: USING THE HANGING-DROP VAPOR DIFFUSION TECHIQUE. 20MG/ML OF PROTEIN WAS MIXED IN EQUAL VOLUMES WITH A CRYSTALLIZATION BUFFER OF 0.1M TRIS/HCL PH 8.5, 0.2 M SODIUM CITRATE, 30% PEG 400) | |||||||||||||||||||||||||
Crystal grow | *PLUS pH: 8.5 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.95372 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 15, 2002 / Details: BENT + TOROIDAL |
Radiation | Monochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95372 Å / Relative weight: 1 |
Reflection | Resolution: 1.94→30 Å / Num. obs: 12124 / % possible obs: 99.5 % / Redundancy: 9 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 32 |
Reflection shell | Resolution: 1.94→2 Å / Redundancy: 7 % / Rmerge(I) obs: 0.477 / Mean I/σ(I) obs: 7.3 / % possible all: 99.3 |
Reflection | *PLUS Num. measured all: 108633 |
Reflection shell | *PLUS Lowest resolution: 2.01 Å / % possible obs: 99.3 % |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.94→30 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.921 / SU B: 1.981 / SU ML: 0.058 / Cross valid method: THROUGHOUT / ESU R: 0.112 / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES FROM BOTH THE N- AND C-TERMINII WERE NOT VISIBLE IN THE ELECTRON DENSITY. THESE RESIDUES WERE OMITTED FROM THE MODEL. THE REFINED ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES FROM BOTH THE N- AND C-TERMINII WERE NOT VISIBLE IN THE ELECTRON DENSITY. THESE RESIDUES WERE OMITTED FROM THE MODEL. THE REFINED MODEL CONTAINS RESIDUES 7- 73. RESIDUES 7-10 OF THE N-TERMINUS ARE NOT IN WELL DEFINED ELECTRON DENSITY. UNACCOUNTED SOLVENT DENSITY IS LOCATED CLOSE TO RESIDUES TYR18 AND TRP35
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL PLUS MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.71 Å2
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Refinement step | Cycle: LAST / Resolution: 1.94→30 Å
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