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- PDB-1ucr: Three-dimensional crystal structure of dissimilatory sulfite redu... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1ucr | ||||||
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Title | Three-dimensional crystal structure of dissimilatory sulfite reductase D (DsrD) | ||||||
![]() | Protein dsvD | ||||||
![]() | UNKNOWN FUNCTION / dissimilatory sulfite reductase D / DNA binding motif / sulfate-reducing bacteria / winged-helix motif | ||||||
Function / homology | Dissimilatory sulphite reductase D / Dissimilatory sulfite reductase D (DsrD) / 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 / Protein DsvD![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Mizuno, N. / Voordouw, G. / Miki, K. / Sarai, A. / Higuchi, Y. | ||||||
![]() | ![]() Title: Crystal Structure of Dissimilatory Sulfite Reductase D (DsrD) Protein-Possible Interaction with B- and Z-DNA by Its Winged-Helix Motif Authors: Mizuno, N. / Voordouw, G. / Miki, K. / Sarai, A. / Higuchi, Y. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 82.7 KB | Display | ![]() |
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PDB format | ![]() | 62.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 388.9 KB | Display | ![]() |
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Full document | ![]() | 391.8 KB | Display | |
Data in XML | ![]() | 5.3 KB | Display | |
Data in CIF | ![]() | 8.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 8841.918 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.5 % | ||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.3 Details: 73-75% saturated ammonium sulfate, pH 5.3, VAPOR DIFFUSION, SITTING DROP, temperature 293K | ||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop / Details: Mizuno, N., (2000) Acta Crystallogr., D56, 754. | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 2, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.708 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→100 Å / Num. obs: 55639 |
Reflection | *PLUS Highest resolution: 1.2 Å / % possible obs: 99.8 % / Num. measured all: 565339 / Rmerge(I) obs: 0.06 |
Reflection shell | *PLUS Highest resolution: 1.2 Å / Lowest resolution: 1.26 Å / % possible obs: 99.8 % / Num. unique obs: 8364 / Num. measured obs: 82965 / Rmerge(I) obs: 0.185 / Mean I/σ(I) obs: 1.1 |
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Processing
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Refinement | Method to determine structure: ![]()
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Refine analyze | Num. disordered residues: 6 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 1451 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.2→10 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL / Version: 97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 10 Å / Rfactor Rwork: 0.1389 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 1.2 Å / Lowest resolution: 1.24 Å / Rfactor Rwork: 0.166 / Num. reflection obs: 5001 |