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- PDB-4hif: Ultrahigh-resolution crystal structure of Z-DNA in complex with Z... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4hif | ||||||||||||||||||||
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Title | Ultrahigh-resolution crystal structure of Z-DNA in complex with Zn2+ ions | ||||||||||||||||||||
![]() | DNA (5'-D(*![]() ![]() ![]() Function / homology | SPERMINE (FULLY PROTONATED FORM) / | ![]() ![]() Biological species | synthetic construct (others) | Method | ![]() ![]() ![]() ![]() Drozdzal, P. / Gilski, M. / Kierzek, R. / Lomozik, L. / Jaskolski, M. | ![]() ![]() 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: ![]() 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: ![]() Title: Anomalous signal of phosphorus used for phasing DNA oligomer: importance of data redundancy Authors: Dauter, Z. / Adamiak, D.A. History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 28.2 KB | Display | ![]() |
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PDB format | ![]() | 19.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4higC ![]() 1i0tS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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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 | #3: Chemical | ChemComp-CL / | ![]() #4: Chemical | ChemComp-SPK / | ![]() #5: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.53 Å3/Da / Density % sol: 19.8 % |
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Crystal grow![]() | Temperature: 292 K / pH: 6 Details: A 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: A 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 ZN2+ SOAKING A CRYSTAL WAS PLACED IN 0.002 ML OF THE RESERVOIR SOLUTION MIXED WITH 0.002 ML OF 5 MM ZNCL2 FOR ONE WEEK. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR555 FLAT PANEL / Detector: IMAGE PLATE / Date: Dec 2, 2010 |
Radiation | Monochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 0.849→17.976 Å / Num. obs: 36512 / % possible obs: 87.9 % / Observed criterion σ(I): -3 / Redundancy: 3.02 % / Biso Wilson estimate: 8.109 Å2 / Rmerge(I) obs: 0.036 / Net I/σ(I): 20.02 |
Reflection shell | Resolution: 0.85→0.9 Å / Redundancy: 1.77 % / Rmerge(I) obs: 0.222 / Mean I/σ(I) obs: 3.11 / % possible all: 63.8 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 1I0T Resolution: 0.85→17.976 Å / Num. parameters: 3228 / Num. restraintsaints: 709 / Cross valid method: FREE R / Stereochemistry target values: CLOWNEY, GELBIN & PARKINSON Details: THE REFINEMENT WAS CARRIED OUT AGAINST SEPARATE BIJVOET PAIRS. ANISOTROPIC ADPS. ANISOTROPIC REFINEMENT REDUCED FREE R-FACTOR FROM 0.1562 TO 0.1235. 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 0.1562 TO 0.1235. HYDROGEN ATOMS WERE ADDED AT RIDING POSITIONS. THE FINAL REFINEMENT WAS CALCULATED USING WEIGHTED FULL MATRIX LEAST-SQUARES PROCEDURE.
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Solvent computation | Solvent model: MOEWS & KRETSINGER, J.MOL.BIOL.(1975) 91, 201 | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 6 / Occupancy sum hydrogen: 144.6 / Occupancy sum non hydrogen: 313.39 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.85→17.976 Å
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Refine LS restraints |
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