+Open data
-Basic information
Entry | Database: PDB / ID: 1uvh | ||||||
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Title | X-ray structure of Dps from Mycobacterium smegmatis | ||||||
Components | STARVATION-INDUCED DNA PROTECTING PROTEIN | ||||||
Keywords | DNA BINDING PROTEIN / DNA PROTECTION FROM OXIDATIVE DAMAGE | ||||||
Function / homology | Function and homology information Oxidoreductases; Oxidizing metal ions / oxidoreductase activity, acting on metal ions / nucleoid / ferric iron binding / intracellular iron ion homeostasis / DNA binding / cytoplasm Similarity search - Function | ||||||
Biological species | MYCOBACTERIUM SMEGMATIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Ilari, A. / Ceci, P. / Falvo, E. / Chiancone, E. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2005 Title: Reassessment of Protein Stability, DNA Binding, and Protection of Mycobacterium Smegmatis Dps. Authors: Ceci, P. / Ilari, A. / Falvo, E. / Giangiacomo, L. / Chiancone, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1uvh.cif.gz | 133.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1uvh.ent.gz | 105.8 KB | Display | PDB format |
PDBx/mmJSON format | 1uvh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1uvh_validation.pdf.gz | 453.6 KB | Display | wwPDB validaton report |
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Full document | 1uvh_full_validation.pdf.gz | 499.9 KB | Display | |
Data in XML | 1uvh_validation.xml.gz | 29.7 KB | Display | |
Data in CIF | 1uvh_validation.cif.gz | 39.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uv/1uvh ftp://data.pdbj.org/pub/pdb/validation_reports/uv/1uvh | HTTPS FTP |
-Related structure data
Related structure data | 1dpsS 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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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 20298.809 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MYCOBACTERIUM SMEGMATIS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8VP75, UniProt: P0C558*PLUS #2: Chemical | ChemComp-FE / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54 % |
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Crystal grow | pH: 7.5 Details: HEPES 0.1 M, IN A PH RANGE BETWEEN 7.0-7.8. AMMONIUM SULFATE IN A RANGE BETWEEN 1.5-2.0 M |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1.2 |
Detector | Date: Jun 15, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.2 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→40 Å / Num. obs: 22346 / % possible obs: 99 % / Redundancy: 10 % / Rmerge(I) obs: 0.082 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1DPS Resolution: 2.8→40 Å / Cross valid method: THROUGHOUT Details: COORDINATES FOR A COMPLETE DODECAMER REPRESENTING THE KNOWN BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE MOLECULE CAN BE GENERATED BY APPLYING CRYSTALLOGRAPHIC SYMMETRY OPERATIONS ...Details: COORDINATES FOR A COMPLETE DODECAMER REPRESENTING THE KNOWN BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE MOLECULE CAN BE GENERATED BY APPLYING CRYSTALLOGRAPHIC SYMMETRY OPERATIONS GIVEN BELOW TO THE TETRAMER OF THE ASYMMETRIC UNIT: SYMGEN X,Y,Z SYMGEN Y-X, 1-X,Z SYMGEN 1-Y,1+X-Y,Z
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Refinement step | Cycle: LAST / Resolution: 2.8→40 Å
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