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Yorodumi- PDB-1wd0: Crystal structures of the hyperthermophilic chromosomal protein S... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1wd0 | ||||||
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Title | Crystal structures of the hyperthermophilic chromosomal protein Sac7d in complex with DNA decamers | ||||||
Components |
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Keywords | structural protein/DNA / Protein-DNA complex / structural protein-DNA COMPLEX | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Sulfolobus acidocaldarius (acidophilic) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Ko, T.-P. / Chu, H.-M. / Chen, C.-Y. / Chou, C.-C. / Wang, A.H.-J. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2004 Title: Structures of the hyperthermophilic chromosomal protein Sac7d in complex with DNA decamers. Authors: Ko, T.P. / Chu, H.M. / Chen, C.Y. / 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 | 1wd0.cif.gz | 40 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1wd0.ent.gz | 25.4 KB | Display | PDB format |
PDBx/mmJSON format | 1wd0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wd/1wd0 ftp://data.pdbj.org/pub/pdb/validation_reports/wd/1wd0 | HTTPS FTP |
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-Related structure data
Related structure data | 1wd1C 1azpS S: Starting model for refinement 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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Details | monomer Sac7d is bound to DNA, DNA forms virtual double helices |
-Components
#1: DNA chain | Mass: 3044.016 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: Protein | | Mass: 7626.914 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfolobus acidocaldarius (acidophilic) Plasmid: pET-3b / 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: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.8 Å3/Da / Density % sol: 30 % | ||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: Tris-HCl, PEG400, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-002 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Feb 7, 2003 |
Radiation | Monochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→30 Å / Num. all: 8617 / Num. obs: 8591 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Rmerge(I) obs: 0.045 / Net I/σ(I): 43 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2.3 / Num. unique all: 827 / % possible all: 97.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb 1azp Resolution: 1.9→30 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 38.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.97 Å / Rfactor Rfree error: 0.017
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