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Yorodumi- PDB-2b1d: 5'-D(*GP*CP*AP*GP*AP*CP*GP*TP*CP*TP*GP*C)-3' Methionine Repressor... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2b1d | ||||||||||||||||||
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Title | 5'-D(*GP*CP*AP*GP*AP*CP*GP*TP*CP*TP*GP*C)-3' Methionine Repressor binding site | ||||||||||||||||||
Components | 5'-D(*Keywords | DNA / sequence dependent DNA deformability / protein-DNA recognition | Function / homology | COBALT HEXAMMINE(III) / DNA / DNA (> 10) | Function and homology information Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | Authors | Berman, H.M. / Locasale, J.W. / Napoli, A.A. | Citation | Journal: J.Mol.Biol. / Year: 2009 | Title: Signatures of protein-DNA recognition in free DNA binding sites. Authors: Locasale, J.W. / Napoli, A.A. / Chen, S. / Berman, H.M. / Lawson, C.L. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2b1d.cif.gz | 52.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2b1d.ent.gz | 36.8 KB | Display | PDB format |
PDBx/mmJSON format | 2b1d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b1/2b1d ftp://data.pdbj.org/pub/pdb/validation_reports/b1/2b1d | HTTPS FTP |
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-Related structure data
Related structure data | 1hq7C 2b1bC 2b1cC 423dS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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-Components
#1: DNA chain | Mass: 3663.392 Da / Num. of mol.: 6 / Source method: obtained synthetically #2: Chemical | #3: Chemical | ChemComp-MG / | #4: 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: 2.87 Å3/Da / Density % sol: 56.8 % | ||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: MPD, sodium cacodylate, cobalt hexamine, magnesium chloride, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K | ||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1.1004 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 26, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1004 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→99 Å / Num. all: 7790 / Num. obs: 7790 / % possible obs: 97.7 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.088 / Χ2: 1.483 |
Reflection shell | Resolution: 2.5→2.57 Å / % possible obs: 97.6 % / Rmerge(I) obs: 0.199 / Num. measured obs: 614 / Χ2: 1.936 / % possible all: 97.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: NDB ID BD0001 (PDB ID 423D) Resolution: 2.5→39.84 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.925 / SU B: 13.384 / SU ML: 0.282 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.787 / ESU R Free: 0.343 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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 WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 51.029 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→39.84 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.885 Å / Total num. of bins used: 4 /
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Label seq-ID: 1 - 12
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