[English] 日本語
Yorodumi- PDB-4hig: Ultrahigh-resolution crystal structure of Z-DNA in complex with M... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4hig | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Ultrahigh-resolution crystal structure of Z-DNA in complex with Mn2+ ion. | ||||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / self-complementary DNA / Z-DNA | Function / homology | : / SPERMINE (FULLY PROTONATED FORM) / DNA | Function and homology information Biological species | synthetic construct (others) | Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.75 Å | Authors | Drozdzal, P. / Gilski, M. / Kierzek, R. / Lomozik, L. / Jaskolski, M. | Citation | 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. #1: 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. #2: Journal: Acta Crystallogr.,Sect.D / Year: 2001 Title: Anomalous signal of phosphorus used for phasing DNA oligomer: importance of data redundancy. Authors: Dauter, Z. / Adamiak, D.A. History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4hig.cif.gz | 28.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4hig.ent.gz | 18.9 KB | Display | PDB format |
PDBx/mmJSON format | 4hig.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hi/4hig ftp://data.pdbj.org/pub/pdb/validation_reports/hi/4hig | HTTPS FTP |
---|
-Related structure data
Related structure data | 4hifC 1i0tS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: DNA chain | Mass: 1810.205 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Synthetic construct / Source: (synth.) synthetic construct (others) #2: Chemical | ChemComp-SPK / | #3: Chemical | ChemComp-MN / | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
---|
-Sample preparation
Crystal | Density Matthews: 1.59 Å3/Da / Density % sol: 22.7 % |
---|---|
Crystal grow | Temperature: 292 K / pH: 6 Details: 1.5 MM DNA WATER SOLUTION MIXED 1:1 V/V WITH 10% MPD, 12 MM SPERMINE TETRA-HCL, 12 MM NACL, 80 MM KCL AND EQUILIBRATED AGAINST 35% MPD, PH 6. VAPOR DIFFUSION, HANGING DROP METHOD, ...Details: 1.5 MM DNA WATER SOLUTION MIXED 1:1 V/V WITH 10% MPD, 12 MM SPERMINE TETRA-HCL, 12 MM NACL, 80 MM KCL AND EQUILIBRATED AGAINST 35% MPD, PH 6. VAPOR DIFFUSION, HANGING DROP METHOD, TEMPERATURE 292K. FOR MN2+ SOAKING, A CRYSTAL WAS PLACED IN 0.002 ML OF THE RESERVOIR SOLUTION MIXED WITH 0.002 ML OF 5 MM MNCL2 FOR ONE WEEK. |
-Data collection
Diffraction |
| ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source |
| ||||||||||||||||||
Detector |
| ||||||||||||||||||
Radiation |
| ||||||||||||||||||
Radiation wavelength |
| ||||||||||||||||||
Reflection | Resolution: 0.75→25.57 Å / Num. obs: 47730 / % possible obs: 79.9 % / Observed criterion σ(I): -3 / Redundancy: 3.28 % / Biso Wilson estimate: 4.756 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 19.28 | ||||||||||||||||||
Reflection shell | Resolution: 0.75→0.77 Å / Redundancy: 1.15 % / Rmerge(I) obs: 0.038 / Mean I/σ(I) obs: 11.39 / % possible all: 10.6 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1I0T Resolution: 0.75→25.57 Å / Num. parameters: 3409 / Num. restraintsaints: 1139 / Cross valid method: FREE R Details: THE REFINEMENT WAS CARRIED OUT AGAINST SEPARATE BIJVOET PAIRS. ANISOTROPIC ADPS. ANISOTROPIC REFINEMENT REDUCED FREE R-FACTOR FROM 0.1295 TO 0.0903. HYDROGEN ATOMS WERE ADDED AT RIDING ...Details: THE REFINEMENT WAS CARRIED OUT AGAINST SEPARATE BIJVOET PAIRS. ANISOTROPIC ADPS. ANISOTROPIC REFINEMENT REDUCED FREE R-FACTOR FROM 0.1295 TO 0.0903. HYDROGEN ATOMS WERE ADDED AT RIDING POSITIONS. THE FINAL REFINEMENT WAS CALCULATED USING WEIGHTED FULL MATRIX LEAST-SQUARES PROCEDURE.
| |||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: MOEWS & KRETSINGER, J.MOL.BIOL.(1975) 91, 201. | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 1 / Occupancy sum hydrogen: 164 / Occupancy sum non hydrogen: 332.97 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.75→25.57 Å
| |||||||||||||||||||||||||||||||||
Refine LS restraints |
|