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Yorodumi- PDB-1wvl: Crystal Structure of Multimeric DNA-binding Protein Sac7d-GCN4 wi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1wvl | ||||||
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Title | Crystal Structure of Multimeric DNA-binding Protein Sac7d-GCN4 with DNA decamer | ||||||
Components |
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Keywords | STRUCTURAL PROTEIN/DNA / leucine zipper / protein engineering / synchrotron radiation / thermophile / STRUCTURAL PROTEIN-DNA COMPLEX | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Sulfolobus acidocaldarius (acidophilic) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Wu, S.W. / Wang, A.H. | ||||||
Citation | Journal: Proteins / Year: 2005 Title: Design and characterization of a multimeric DNA binding protein using Sac7d and GCN4 as templates Authors: Wu, S.W. / Ko, T.P. / Chou, C.C. / Wang, A.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1wvl.cif.gz | 60.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1wvl.ent.gz | 41.9 KB | Display | PDB format |
PDBx/mmJSON format | 1wvl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wv/1wvl ftp://data.pdbj.org/pub/pdb/validation_reports/wv/1wvl | HTTPS FTP |
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-Related structure data
Related structure data | 1azpS S: Starting model for refinement |
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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 on special symmetry positions |
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Details | The biological assembly is a tetramer generated from the dimer in the asymmetric unit by the operations: -1+y, 1+x, 3/4-z. |
-Components
#1: DNA chain | Mass: 3044.016 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: Protein | Mass: 9218.810 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfolobus acidocaldarius (acidophilic) Plasmid: pET-11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P13123 #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 3.27 Å3/Da / Density % sol: 62.35 % | ||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 1.6M Tri-Sodium Citrate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 116 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Apr 30, 2003 |
Radiation | Monochromator: MSC confocal optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→20 Å / Num. all: 11603 / Num. obs: 10690 / % possible obs: 99.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 |
Reflection shell | Resolution: 2.6→2.7 Å / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1azp Resolution: 2.6→20 Å / Cross valid method: THROUGHOUT / σ(F): 3 / Stereochemistry target values: Engh & Huber
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.6→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.76 Å / Rfactor Rfree error: 0.046
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