+Open data
-Basic information
Entry | Database: PDB / ID: 2zud | ||||||
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Title | Crystal Structure of Left-handed RadA Filament | ||||||
Components | DNA repair and recombination protein radA | ||||||
Keywords | RECOMBINATION / Archaea / Left-handed helical filament / DNA-binding / RecA / Rad51 / Dmc1 / ATP-binding / DNA damage / DNA recombination / Nucleotide-binding | ||||||
Function / homology | Function and homology information ATP-dependent DNA damage sensor activity / DNA recombination / damaged DNA binding / DNA repair / ATP hydrolysis activity / ATP binding Similarity search - Function | ||||||
Biological species | Sulfolobus solfataricus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å | ||||||
Authors | Chang, Y.W. / Ko, T.P. / Wang, T.F. / Wang, A.H.J. | ||||||
Citation | Journal: Plos One / Year: 2009 Title: Three new structures of left-handed RADA helical filaments: structural flexibility of N-terminal domain is critical for recombinase activity Authors: Chang, Y.W. / Ko, T.P. / Lee, C.D. / Chang, Y.C. / Lin, K.A. / Chang, C.S. / Wang, A.H.J. / Wang, T.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2zud.cif.gz | 123.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2zud.ent.gz | 97.9 KB | Display | PDB format |
PDBx/mmJSON format | 2zud.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zu/2zud ftp://data.pdbj.org/pub/pdb/validation_reports/zu/2zud | HTTPS FTP |
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-Related structure data
Related structure data | 2zubC 2zucC 2dflS S: Starting model for refinement C: citing same article (ref.) |
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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: 35914.031 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Gene: rada / Plasmid: pET 32 Xa/LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q55075 #2: 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: 2.77 Å3/Da / Density % sol: 55.53 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 2M Sodium Formate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL12B2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 7, 2007 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→30 Å / Num. all: 13730 / Num. obs: 13493 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 5.9 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 25.3 |
Reflection shell | Resolution: 3.2→3.31 Å / Redundancy: 6 % / Rmerge(I) obs: 0.474 / Mean I/σ(I) obs: 5 / Num. unique all: 1318 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2DFL Resolution: 3.2→30 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 54.8 Å2 | |||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.2→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.2→3.31 Å / Rfactor Rfree error: 0.111
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