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Yorodumi- PDB-1azp: HYPERTHERMOPHILE CHROMOSOMAL PROTEIN SAC7D BOUND WITH KINKED DNA ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1azp | ||||||
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Title | HYPERTHERMOPHILE CHROMOSOMAL PROTEIN SAC7D BOUND WITH KINKED DNA DUPLEX | ||||||
Components |
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Keywords | DNA BINDING PROTEIN/DNA / COMPLEX (CHROMATIN PROTEIN-DNA) / DNA-BINDING / ARCHEA KINKED-DNA / MINOR-GROOVE BINDING / INTERCALATION / DNA BINDING PROTEIN-DNA COMPLEX | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Sulfolobus acidocaldarius (acidophilic) | ||||||
Method | X-RAY DIFFRACTION / MIR / Resolution: 1.6 Å | ||||||
Authors | Robinson, H. / Gao, Y.-G. / Mccrary, B.S. / Edmondson, S.P. / Shriver, J.W. / Wang, A.H.-J. | ||||||
Citation | Journal: Nature / Year: 1998 Title: The hyperthermophile chromosomal protein Sac7d sharply kinks DNA. Authors: Robinson, H. / Gao, Y.G. / McCrary, B.S. / Edmondson, S.P. / Shriver, J.W. / 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 | 1azp.cif.gz | 42 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1azp.ent.gz | 27.1 KB | Display | PDB format |
PDBx/mmJSON format | 1azp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1azp_validation.pdf.gz | 421.6 KB | Display | wwPDB validaton report |
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Full document | 1azp_full_validation.pdf.gz | 422.5 KB | Display | |
Data in XML | 1azp_validation.xml.gz | 7.3 KB | Display | |
Data in CIF | 1azp_validation.cif.gz | 9.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/az/1azp ftp://data.pdbj.org/pub/pdb/validation_reports/az/1azp | HTTPS FTP |
-Related 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: 7626.914 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfolobus acidocaldarius (acidophilic) Production host: Escherichia coli (E. coli) / 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: 2.81 Å3/Da / Density % sol: 56 % | ||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 6.5 / Details: pH 6.5, VAPOR DIFFUSION, HANGING DROP | ||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 123 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.540598 |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Jul 15, 1997 |
Radiation | Monochromator: GRAPHITE / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.540598 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→30 Å / Num. obs: 18497 / % possible obs: 95 % / Observed criterion σ(I): 1 / Redundancy: 6.6 % / Biso Wilson estimate: 19.4 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 11.1 |
Reflection shell | Resolution: 1.6→1.65 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.393 / Mean I/σ(I) obs: 1.5 / % possible all: 95.2 |
Reflection shell | *PLUS % possible obs: 95.2 % |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 1.6→6 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.001 / Cross valid method: A POSTERIORI / σ(F): 3
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Refinement step | Cycle: LAST / Resolution: 1.6→6 Å
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Refine LS restraints |
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.84 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |