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Yorodumi- PDB-1pup: CRYSTAL STRUCTURE OF A PEPTIDE NUCLEIC ACID (PNA) DUPLEX AT 1.7 A... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1pup | |||||||||||||||||||||
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Title | CRYSTAL STRUCTURE OF A PEPTIDE NUCLEIC ACID (PNA) DUPLEX AT 1.7 ANGSTROMS RESOLUTION | |||||||||||||||||||||
Components | PNA (H-P(*Keywords | PEPTIDE NUCLEIC ACID / DNA ANALOGUE / DOUBLE HELIX | Function / homology | DNA | Function and homology information Method | X-RAY DIFFRACTION / SIR / Resolution: 1.7 Å | Authors | Rasmussen, H. / Kastrup, J.S. | Citation | Journal: Nat.Struct.Biol. / Year: 1997 Title: Crystal structure of a peptide nucleic acid (PNA) duplex at 1.7 A resolution. Authors: Rasmussen, H. / Kastrup, J.S. / Nielsen, J.N. / Nielsen, J.M. / Nielsen, P.E. #1: Journal: Science / Year: 1995 Title: A Nucleic Acid Triple Helix Formed by a Peptide Nucleic Acid-DNA Complex Authors: Betts, L. / Josey, J.A. / Veal, J.M. / Jordan, S.R. #2: Journal: Nat.Struct.Biol. / Year: 1996 Title: Solution Structure of a Petide Nucleic Acid-DNA Duplex Authors: Eriksson, M. / Nielsen, P.E. #3: Journal: Science / Year: 1994 Title: NMR Solution Structure of a Peptide Nucleic Acid Complexed with RNA Authors: Brown, S.C. / Thomson, S.A. / Veal, J.M. / Davis, D.G. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1pup.cif.gz | 17.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1pup.ent.gz | 12.7 KB | Display | PDB format |
PDBx/mmJSON format | 1pup.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1pup_validation.pdf.gz | 331.3 KB | Display | wwPDB validaton report |
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Full document | 1pup_full_validation.pdf.gz | 339.7 KB | Display | |
Data in XML | 1pup_validation.xml.gz | 2.6 KB | Display | |
Data in CIF | 1pup_validation.cif.gz | 3.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pu/1pup ftp://data.pdbj.org/pub/pdb/validation_reports/pu/1pup | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: DNA chain | Mass: 1585.633 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source #2: 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: 2.51 Å3/Da / Density % sol: 51.01 % Description: DERIVATIVE DATA WERE COLLECTED AT EMBL, HAMBURG AT BEAMLINE X31 TO 1.9 A RESOLUTION. | |||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 7 / Details: pH 7.00, VAPOR DIFFUSION, HANGING DROP | |||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 20 ℃Details: drop solution was mixed with an equal volume of reservoir solution | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 285 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Sep 1, 1995 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 1.7→25 Å / Num. obs: 5222 / % possible obs: 77 % / Observed criterion σ(I): 1 / Redundancy: 1.9 % / Biso Wilson estimate: 15.8 Å2 / Rmerge(I) obs: 0.032 / Net I/σ(I): 13.1 |
Reflection shell | Resolution: 1.7→1.9 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.058 / Mean I/σ(I) obs: 7.3 / % possible all: 37 |
Reflection | *PLUS Highest resolution: 1.7 Å / Lowest resolution: 25 Å / % possible obs: 77 % / Redundancy: 1.9 % |
Reflection shell | *PLUS Highest resolution: 1.7 Å / Lowest resolution: 1.9 Å / % possible obs: 37 % |
-Processing
Software |
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Refinement | Method to determine structure: SIR / Resolution: 1.7→6 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / σ(F): 2
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Displacement parameters | Biso mean: 11.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine Biso |
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Refinement step | Cycle: LAST / Resolution: 1.7→6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.78 Å / Total num. of bins used: 8
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Xplor file | Serial no: 1 / Param file: PARAM.PNA / Topol file: TOPH_JULY96.PNA | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.7 Å / Lowest resolution: 6 Å / σ(F): 2 / % reflection Rfree: 10 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor obs: 0.285 |