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Yorodumi- PDB-1en9: 1A CRYSTAL STRUCTURES OF B-DNA REVEAL SEQUENCE-SPECIFIC BINDING A... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1en9 | ||||||||||||||||||
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Title | 1A CRYSTAL STRUCTURES OF B-DNA REVEAL SEQUENCE-SPECIFIC BINDING AND GROOVE-SPECIFIC BENDING OF DNA BY MAGNESIUM AND CALCIUM. | ||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / divalent cations / DNA sequence-specific binding / shelxdna / B-DNA | Function / homology | DNA | Function and homology information Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.985 Å | Authors | Chiu, T.K. / Dickerson, R.E. | Citation | Journal: J.Mol.Biol. / Year: 2000 Title: 1 A crystal structures of B-DNA reveal sequence-specific binding and groove-specific bending of DNA by magnesium and calcium. Authors: Chiu, T.K. / Dickerson, R.E. #1: Journal: J.Mol.Biol. / Year: 1999 Title: Absence of minor groove monovalent cations in the crosslinked dodecamer CGCGAATTCGCG Authors: Chiu, T.K. / Kaczor-Grzeskowiak, M. / Dickerson, R.E. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1en9.cif.gz | 32.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1en9.ent.gz | 22.3 KB | Display | PDB format |
PDBx/mmJSON format | 1en9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1en9_validation.pdf.gz | 384.9 KB | Display | wwPDB validaton report |
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Full document | 1en9_full_validation.pdf.gz | 390.1 KB | Display | |
Data in XML | 1en9_validation.xml.gz | 4.2 KB | Display | |
Data in CIF | 1en9_validation.cif.gz | 5.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/en/1en9 ftp://data.pdbj.org/pub/pdb/validation_reports/en/1en9 | HTTPS FTP |
-Related structure data
Related structure data | 1en3C 1en8C 1eneC C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: DNA chain | Mass: 3045.992 Da / Num. of mol.: 1 / Source method: obtained synthetically | ||
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#2: Chemical | ChemComp-MG / #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.06 Å3/Da / Density % sol: 36.88 % | |||||||||||||||||||||||||
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Crystal grow | Temperature: 275 K / Method: vapor diffusion, sitting drop Details: initial concentration in droplet: 0.17 mM dna, 31.40 mM magnesium acetate 0.28 mM streptonigrin, 10-15% MPD, 30% final MPD concentration in reservoir. Solutions were unbuffered, VAPOR ...Details: initial concentration in droplet: 0.17 mM dna, 31.40 mM magnesium acetate 0.28 mM streptonigrin, 10-15% MPD, 30% final MPD concentration in reservoir. Solutions were unbuffered, VAPOR DIFFUSION, SITTING DROP, temperature 275.0K | |||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 4 ℃ | |||||||||||||||||||||||||
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: NSLS / Beamline: X8C / Wavelength: 0.95 |
Detector | Type: MARRESEARCH / Detector: AREA DETECTOR / Date: Nov 19, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95 Å / Relative weight: 1 |
Reflection | Resolution: 0.985→8 Å / Num. all: 13087 / Num. obs: 13087 / % possible obs: 93.3 % / Observed criterion σ(I): -1 / Redundancy: 4.87 % / Biso Wilson estimate: 5.82 Å2 / Rmerge(I) obs: 0.031 / Net I/σ(I): 32.8 |
Reflection shell | Resolution: 0.985→1.016 Å / Rmerge(I) obs: 0.122 / Mean I/σ(I) obs: 6.9 / Num. unique all: 1253 / % possible all: 89.5 |
Reflection | *PLUS Num. measured all: 63745 |
Reflection shell | *PLUS % possible obs: 89.5 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: BDJ019 Resolution: 0.985→8 Å / Num. parameters: 16139 / Num. restraintsaints: 5024 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Parkinson et al. Details: REFINEMENT STARTED IN X-PLOR 3.843 WITH DNA MODEL FROM BDJ019. AFTER ALL DATA HAS BEEN ADDED AND REFINED BY SIMULATED ANNEALING IN X-PLOR 3.843, REFINEMENT CONTINUED BY CONJUGATE GRADIENT ...Details: REFINEMENT STARTED IN X-PLOR 3.843 WITH DNA MODEL FROM BDJ019. AFTER ALL DATA HAS BEEN ADDED AND REFINED BY SIMULATED ANNEALING IN X-PLOR 3.843, REFINEMENT CONTINUED BY CONJUGATE GRADIENT LEAST-SQUARES IN SHELXL-97. THE TOP 50 MOST DISAGREEABLE REFLECTIONS WERE REJECTED TOWARDS THE LATTER STAGES OF REFINEMENT BUT THESE ARE STILL INCLUDED IN THE RELEASED DATA.
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Solvent computation | Solvent model: SHELX swat option | |||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 9 / Occupancy sum hydrogen: 113 / Occupancy sum non hydrogen: 271.4 | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.985→8 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL-97 / Classification: refinement | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.184 / Rfactor Rwork: 0.1653 |