+Open data
-Basic information
Entry | Database: PDB / ID: 1dvb | ||||||
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Title | RUBRERYTHRIN | ||||||
Components | RUBRERYTHRIN | ||||||
Keywords | ELECTRON TRANSPORT / IRON / FERROXIDASE | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Desulfovibrio vulgaris subsp. vulgaris str. Hildenborough (bacteria) | ||||||
Method | X-RAY DIFFRACTION / COORDINATES FROM PDB / Resolution: 1.9 Å | ||||||
Authors | Sieker, L.C. / Holmes, M. / Le Trong, I. / Turley, S. / Liu, M.Y. / Legall, J. / Stenkamp, R.E. | ||||||
Citation | Journal: J.Biol.Inorg.Chem. / Year: 2000 Title: The 1.9 A crystal structure of the "as isolated" rubrerythrin from Desulfovibrio vulgaris: some surprising results. Authors: Sieker, L.C. / Holmes, M. / Le Trong, I. / Turley, S. / Liu, M.Y. / LeGall, J. / Stenkamp, R.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1dvb.cif.gz | 57.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dvb.ent.gz | 40.2 KB | Display | PDB format |
PDBx/mmJSON format | 1dvb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1dvb_validation.pdf.gz | 416.8 KB | Display | wwPDB validaton report |
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Full document | 1dvb_full_validation.pdf.gz | 425.3 KB | Display | |
Data in XML | 1dvb_validation.xml.gz | 12.3 KB | Display | |
Data in CIF | 1dvb_validation.cif.gz | 17.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dv/1dvb ftp://data.pdbj.org/pub/pdb/validation_reports/dv/1dvb | HTTPS FTP |
-Related structure data
Related structure data | 1rytS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 21577.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Desulfovibrio vulgaris subsp. vulgaris str. Hildenborough (bacteria) Species: Desulfovibrio vulgaris / Strain: HILDENBOROUGH / References: UniProt: P24931 | ||||
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#2: Chemical | #3: Chemical | ChemComp-ZN / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 3 |
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-Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 48.7 % | |||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion / pH: 7.5 Details: PEG4000, Tris acid maleate, pH 7.5, VAPOR DIFFUSION, temperature 277K | |||||||||||||||
Crystal grow | *PLUS pH: 8 / Method: vapor diffusion, hanging drop / Details: deMare, F., (1996) Nat. Struct. Biol., 3, 539. | |||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→20 Å / Num. all: 226047 / Num. obs: 15420 / % possible obs: 87.6 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.093 |
Reflection shell | Resolution: 1.88→2.02 Å |
Reflection | *PLUS Num. measured all: 226047 |
-Processing
Software |
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Refinement | Method to determine structure: COORDINATES FROM PDB Starting model: PDB ID 1RYT Resolution: 1.9→20 Å / Num. parameters: 696 / Num. restraintsaints: 652 / Cross valid method: FREE R / σ(F): 4 / σ(I): 2 / Stereochemistry target values: Engh & Huber
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Refine analyze | Num. disordered residues: 1 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 1652 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→20 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL-97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.9 Å / σ(F): 4 / % reflection Rfree: 5 % / Rfactor Rwork: 0.199 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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