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Yorodumi- PDB-3ft7: Crystal structure of an extremely stable dimeric protein from sul... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ft7 | ||||||
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Title | Crystal structure of an extremely stable dimeric protein from sulfolobus islandicus | ||||||
Components | Uncharacterized protein ORF56 | ||||||
Keywords | DNA BINDING PROTEIN / PLASMID COPY CONTROL PROTEIN / RIBBON HELIX HELIX PROTEIN | ||||||
Function / homology | Met repressor-like / Arc Repressor Mutant / Arc-type ribbon-helix-helix / Ribbon-helix-helix / regulation of DNA-templated transcription / Orthogonal Bundle / Mainly Alpha / CopG domain protein DNA-binding domain protein Function and homology information | ||||||
Biological species | Sulfolobus islandicus (acidophilic) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å | ||||||
Authors | Neumann, P. / Loew, C. / Weininger, U. / Stubbs, M.T. | ||||||
Citation | Journal: Biochemistry / Year: 2009 Title: Structure-Based Stability Analysis of an Extremely Stable Dimeric DNA Binding Protein from Sulfolobus islandicus Authors: Weininger, U. / Zeeb, M. / Neumann, P. / Low, C. / Stubbs, M.T. / Lipps, G. / Balbach, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ft7.cif.gz | 53.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ft7.ent.gz | 37.5 KB | Display | PDB format |
PDBx/mmJSON format | 3ft7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ft7_validation.pdf.gz | 436.2 KB | Display | wwPDB validaton report |
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Full document | 3ft7_full_validation.pdf.gz | 440.3 KB | Display | |
Data in XML | 3ft7_validation.xml.gz | 7.4 KB | Display | |
Data in CIF | 3ft7_validation.cif.gz | 9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ft/3ft7 ftp://data.pdbj.org/pub/pdb/validation_reports/ft/3ft7 | HTTPS FTP |
-Related structure data
Related structure data | 2k9iC 1mykS 1parS C: citing same article (ref.) 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
#1: Protein | Mass: 6536.647 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfolobus islandicus (acidophilic) / Gene: PLASMID PRN1 / Plasmid: PET28C? / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q54323 #2: Chemical | ChemComp-GOL / | #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: 1.7877 Å3/Da / Density % sol: 31.1971 % / Mosaicity: 0.75 ° |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 16-22% PEG 4000, 100mM HEPES pH 7.5 , VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-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: Jul 7, 2007 / Details: mirrors | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection twin | Operator: h,-k,-l / Fraction: 0.481 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2→85.749 Å / Num. obs: 6218 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 26.651 Å2 / Rmerge(I) obs: 0.08 / Rsym value: 0.08 / Net I/σ(I): 6.307 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1MYK, 1PAR Resolution: 2→33.03 Å / Occupancy max: 1 / Occupancy min: 0 / Isotropic thermal model: Isotropic, TLS refinement / Cross valid method: THROUGHOUT / σ(F): 1.47 / σ(I): 0 / Stereochemistry target values: TWIN_LSQ_F
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 89.474 Å2 / ksol: 0.363 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 132.3 Å2 / Biso mean: 49.037 Å2 / Biso min: 9.88 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→33.03 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6 / % reflection obs: 98 %
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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