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Yorodumi- PDB-1ucr: Three-dimensional crystal structure of dissimilatory sulfite redu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ucr | ||||||
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Title | Three-dimensional crystal structure of dissimilatory sulfite reductase D (DsrD) | ||||||
Components | Protein dsvD | ||||||
Keywords | 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 Function and homology information | ||||||
Biological species | Desulfovibrio vulgaris (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.2 Å | ||||||
Authors | Mizuno, N. / Voordouw, G. / Miki, K. / Sarai, A. / Higuchi, Y. | ||||||
Citation | Journal: STRUCTURE / Year: 2003 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ucr.cif.gz | 82.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ucr.ent.gz | 62.8 KB | Display | PDB format |
PDBx/mmJSON format | 1ucr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uc/1ucr ftp://data.pdbj.org/pub/pdb/validation_reports/uc/1ucr | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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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.) Desulfovibrio vulgaris (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q46582 #2: Chemical | ChemComp-SO4 / #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: 2.26 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: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 0.708 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: SIRAS / Resolution: 1.2→10 Å / Num. parameters: 13068 / Num. restraintsaints: 15368 / Cross valid method: THROUGHOUT / σ(F): 4 / Stereochemistry target values: Engh & Huber
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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 |