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Yorodumi- PDB-1wq2: Neutron Crystal Structure Of Dissimilatory Sulfite Reductase D (DsrD) -
+Open data
-Basic information
Entry | Database: PDB / ID: 1wq2 | |||||||||
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Title | Neutron Crystal Structure Of Dissimilatory Sulfite Reductase D (DsrD) | |||||||||
Components | Protein dsvD | |||||||||
Keywords | UNKNOWN FUNCTION / neutron hydrogen hydration protein | |||||||||
Function / homology | Function and homology information 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 Similarity search - Domain/homology | |||||||||
Biological species | Desulfovibrio vulgaris (bacteria) | |||||||||
Method | NEUTRON DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | |||||||||
Authors | Chatake, T. / Mizuno, N. / Voordouw, G. / Higuchi, Y. / Arai, S. / Tanaka, I. / Niimura, N. | |||||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2003 Title: Crystallization and preliminary neutron analysis of the dissimilatory sulfite reductase D (DsrD) protein from the sulfate-reducing bacterium Desulfovibrio vulgaris. Authors: Chatake, T. / Mizuno, N. / Voordouw, G. / Higuchi, Y. / Arai, S. / Tanaka, I. / Niimura, N. #1: Journal: J.Synchrotron Radiat. / Year: 2004 Title: Hydration structures in proteins and neutron diffraction experiment on dissimilatory sul te reductase D (DsrD) Authors: Chatake, T. / Ostermann, A. / Kurihara, K. / Parak, F.G. / Mizuno, N. / Voordouw, G. / Higuchi, Y. / Tanaka, I. / Niimura, N. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1wq2.cif.gz | 62 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1wq2.ent.gz | 46.4 KB | Display | PDB format |
PDBx/mmJSON format | 1wq2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1wq2_validation.pdf.gz | 355.5 KB | Display | wwPDB validaton report |
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Full document | 1wq2_full_validation.pdf.gz | 355.5 KB | Display | |
Data in XML | 1wq2_validation.xml.gz | 4.2 KB | Display | |
Data in CIF | 1wq2_validation.cif.gz | 6.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wq/1wq2 ftp://data.pdbj.org/pub/pdb/validation_reports/wq/1wq2 | HTTPS FTP |
-Related structure data
Related structure data | 1ucrS 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: 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: Chemical | ChemComp-DOD / | |
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-Experimental details
-Experiment
Experiment | Method: NEUTRON DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.3 Details: deuterated ammoniu sulfate, deuterated Tris-HCl, pH 5.3, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Wavelength: 2.88 Å |
Detector | Detector: IMAGE PLATE / Date: May 5, 2003 / Details: monochromator BIX-3 |
Radiation | Monochromator: ellastically bent silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 2.88 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→100 Å / Num. all: 7572 / Num. obs: 7001 / % possible obs: 92.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.143 |
Reflection shell | Resolution: 2.4→2.49 Å / Rmerge(I) obs: 0.395 / Mean I/σ(I) obs: 2.3 / Num. unique all: 534 / % possible all: 82.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1UCR Resolution: 2.4→20 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 18.3 Å2 | |||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→20 Å
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Refine LS restraints |
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