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Yorodumi- PDB-4r15: High-resolution crystal structure of Z-DNA in complex with Cr3+ c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4r15 | ||||||||||||||||||
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Title | High-resolution crystal structure of Z-DNA in complex with Cr3+ cations | ||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / SELF-COMPLEMENTARY DNA / Z-DNA | Function / homology | CHROMIUM ION / DNA | Function and homology information Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.97 Å | Authors | Drozdzal, P. / Gilski, M. / Kierzek, R. / Lomozik, L. / Jaskolski, M. | Citation | Journal: J.Biol.Inorg.Chem. / Year: 2015 Title: High-resolution crystal structure of Z-DNA in complex with Cr(3+) cations. Authors: Drozdzal, P. / Gilski, M. / Kierzek, R. / Lomozik, L. / Jaskolski, M. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2013 Title: Ultrahigh-resolution crystal structures of Z-DNA in complex with Mn(2+) and Zn(2+) ions. Authors: Drozdzal, P. / Gilski, M. / Kierzek, R. / Lomozik, L. / Jaskolski, M. #2: Journal: Acta Crystallogr.,Sect.D / Year: 2014 Title: Phosphates in the Z-DNA dodecamer are flexible, but their P-SAD signal is sufficient for structure solution. Authors: Luo, Z. / Dauter, M. / Dauter, Z. #3: Journal: Nucleic Acids Res. / Year: 2011 Title: High regularity of Z-DNA revealed by ultra high-resolution crystal structure at 0.55 A. Authors: Brzezinski, K. / Brzuszkiewicz, A. / Dauter, M. / Kubicki, M. / Jaskolski, M. / Dauter, Z. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4r15.cif.gz | 28.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4r15.ent.gz | 20.4 KB | Display | PDB format |
PDBx/mmJSON format | 4r15.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r1/4r15 ftp://data.pdbj.org/pub/pdb/validation_reports/r1/4r15 | HTTPS FTP |
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-Related structure data
Related structure data | 4hifS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | Self-complementary dimer of chains A and B |
-Components
#1: DNA chain | Mass: 1810.205 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: SYNTHETIC CONSTRUCT #2: Chemical | #3: 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: 1.66 Å3/Da / Density % sol: 24.88 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6 Details: A 1.5 MM WATER SOLUTION OF DNA MIXED 1:1 V/V WITH 10% MPD, 12 MM SPERMINE*4HCL, 12 MM NACL, 80 MM KCL AND EQUILIBRATED AGAINST 35% MPD, PH 6. FOR CR3+ SOAKING, THE CRYSTAL WAS PLACED FOR ...Details: A 1.5 MM WATER SOLUTION OF DNA MIXED 1:1 V/V WITH 10% MPD, 12 MM SPERMINE*4HCL, 12 MM NACL, 80 MM KCL AND EQUILIBRATED AGAINST 35% MPD, PH 6. FOR CR3+ SOAKING, THE CRYSTAL WAS PLACED FOR SEVERAL DAYS IN 0.002 ML OF THE RESERVOIR SOLUTION MIXED WITH 0.002 ML OF 5 MM [CR(H2O)6]CL3, VAPOR DIFFUSION, HANGING DROP, temperature 292.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Nov 30, 2011 |
Radiation | Monochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 0.97→24.83 Å / Num. all: 26535 / Num. obs: 26535 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.53 % / Biso Wilson estimate: 13.586 Å2 / Rmerge(I) obs: 0.016 / Net I/σ(I): 24.85 |
Reflection shell | Resolution: 0.973→1 Å / Redundancy: 2.14 % / Rmerge(I) obs: 0.432 / Mean I/σ(I) obs: 2.05 / % possible all: 93.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4HIF Resolution: 0.97→24.83 Å / Num. parameters: 3347 / Num. restraintsaints: 6729 / Cross valid method: FREE R StereochEM target val spec case: PHOSPHATE AND GLYCOSIDIC ANGLES ACCORDING TO PDB MODEL 3P4J Stereochemistry target values: CLOWNEY, GELBIN & PARKINSON Details: THE REFINEMENT WAS CARRIED OUT AGAINST SEPARATE BIJVOET PAIRS. ANISOTROPIC ATOMIC DISPLACEMENT PARAMETERS WERE USED. ANISOTROPIC REFINEMENT REDUCED FREE R-FACTOR FROM 0.2585 TO 0.1976. ...Details: THE REFINEMENT WAS CARRIED OUT AGAINST SEPARATE BIJVOET PAIRS. ANISOTROPIC ATOMIC DISPLACEMENT PARAMETERS WERE USED. ANISOTROPIC REFINEMENT REDUCED FREE R-FACTOR FROM 0.2585 TO 0.1976. HYDROGEN ATOMS WERE ADDED AT RIDING POSITION THE FINAL REFINEMENT WAS CALCULATED USING WEIGHTED FULL-MATRIX LEAST-SQUARES PROCEDURE AND ALL REFLECTIONS.
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Solvent computation | Solvent model: MOEWS & KRETSINGER, J.MOL.BIOL.(1975) 91, 201 | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 13 / Occupancy sum hydrogen: 136 / Occupancy sum non hydrogen: 280.78 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.97→24.83 Å
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Refine LS restraints |
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