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Yorodumi- PDB-1sfx: X-ray crystal structure of putative HTH transcription regulator f... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1sfx | ||||||
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Title | X-ray crystal structure of putative HTH transcription regulator from Archaeoglobus fulgidus | ||||||
Components | Conserved hypothetical protein AF2008 | ||||||
Keywords | structural genomics / unknown function / conserved hypothetical protein / HTH motif / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | Function and homology information Transcription regulator TrmB, N-terminal / Sugar-specific transcriptional regulator TrmB / ArsR-like helix-turn-helix domain / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha Similarity search - Domain/homology | ||||||
Biological species | Archaeoglobus fulgidus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.55 Å | ||||||
Authors | Osipiuk, J. / Skarina, T. / Savchenko, A. / Edwards, A. / Cymborowski, M. / Minor, W. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: X-ray crystal structure of putative HTH transcription regulator from Archaeoglobus fulgidus Authors: Osipiuk, J. / Skarina, T. / Savchenko, A. / Edwards, A. / Cymborowski, M. / Minor, W. / Joachimiak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1sfx.cif.gz | 114.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1sfx.ent.gz | 96.2 KB | Display | PDB format |
PDBx/mmJSON format | 1sfx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1sfx_validation.pdf.gz | 439.9 KB | Display | wwPDB validaton report |
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Full document | 1sfx_full_validation.pdf.gz | 440.8 KB | Display | |
Data in XML | 1sfx_validation.xml.gz | 15.1 KB | Display | |
Data in CIF | 1sfx_validation.cif.gz | 23.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sf/1sfx ftp://data.pdbj.org/pub/pdb/validation_reports/sf/1sfx | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Details | Putative biological unit is a dimer |
-Components
#1: Protein | Mass: 12777.522 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Strain: DSM 4304 / Gene: AF2008 / Production host: Escherichia coli (E. coli) / References: UniProt: O28271 #2: Chemical | #3: Chemical | #4: 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: 2.38 Å3/Da / Density % sol: 48.32 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: PEG 8000, Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97926 Å |
Detector | Type: SBC-2 / Detector: CCD / Date: Feb 7, 2004 |
Radiation | Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97926 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→40 Å / Num. all: 34891 / Num. obs: 34193 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 16.1 % / Rmerge(I) obs: 0.104 / Net I/σ(I): 39 |
Reflection shell | Resolution: 1.55→1.59 Å / Rmerge(I) obs: 0.628 / Mean I/σ(I) obs: 2.89 / Num. unique all: 2185 / % possible all: 94.8 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.55→40 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.954 / SU B: 1.336 / SU ML: 0.048 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.106 / ESU R Free: 0.078 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 12.339 Å2
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Refinement step | Cycle: LAST / Resolution: 1.55→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.55→1.59 Å / Total num. of bins used: 20
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