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Yorodumi- PDB-1wto: Hyperthermophile chromosomal protein SAC7D double mutant V26F/M29... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1wto | ||||||
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Title | Hyperthermophile chromosomal protein SAC7D double mutant V26F/M29F in complex with DNA GCGATCGC | ||||||
Components |
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Keywords | DNA BINDING PROTEIN/DNA / COMPLEX CHROMATIN PROTEIN-DNA / MINOR-GROOVE DNA BINDING / ARCHEA / KINKED-DNA / INTERCALATION / Sac7d mutant / DNA BINDING PROTEIN-DNA COMPLEX | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Sulfolobus acidocaldarius (acidophilic) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.5 Å | ||||||
Authors | Chen, C.-Y. / Ko, T.-P. / Lin, T.-W. / Chou, C.-C. / Chen, C.-J. / Wang, A.H.-J. | ||||||
Citation | Journal: NUCLEIC ACIDS RES. / Year: 2005 Title: Probing the DNA kink structure induced by the hyperthermophilic chromosomal protein Sac7d Authors: Chen, C.-Y. / Ko, T.-P. / Lin, T.-W. / Chou, C.-C. / Chen, C.-J. / Wang, A.H.-J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1wto.cif.gz | 36 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1wto.ent.gz | 26.3 KB | Display | PDB format |
PDBx/mmJSON format | 1wto.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wt/1wto ftp://data.pdbj.org/pub/pdb/validation_reports/wt/1wto | HTTPS FTP |
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-Related structure data
Related structure data | 1wtpC 1wtqC 1wtrC 1wtvC 1wtwC 1wtxC 1xyiC C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: DNA chain | Mass: 2427.605 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: Protein | | Mass: 7690.935 Da / Num. of mol.: 1 / Mutation: V26F/M29F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfolobus acidocaldarius (acidophilic) Plasmid: pET3B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P13123 #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: 2.115 Å3/Da / Density % sol: 39.6 % | ||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 Details: PEG 400, Tris buffer, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K | ||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 1.5→40 Å / Num. all: 17486 / Num. obs: 16734 / % possible obs: 95.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 4.3 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 22.7 | ||||||||||||||||||
Reflection shell | Resolution: 1.5→1.55 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.351 / Mean I/σ(I) obs: 4.17 / Num. unique all: 1692 / % possible all: 94.2 |
-Processing
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Refinement | Method to determine structure: MAD / Resolution: 1.5→40 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.5→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.55 Å / Rfactor Rfree error: 0.019
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