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Yorodumi- PDB-3etl: RadA recombinase from Methanococcus maripaludis in complex with AMPPNP -
+Open data
-Basic information
Entry | Database: PDB / ID: 3etl | ||||||
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Title | RadA recombinase from Methanococcus maripaludis in complex with AMPPNP | ||||||
Components | DNA repair and recombination protein radA | ||||||
Keywords | DNA BINDING PROTEIN / RECOMBINATION / RadA / Strand exchange protein / ATPase / recombinase / ATP analogue / ATP-binding / DNA damage / DNA recombination / DNA-binding / Nucleotide-binding | ||||||
Function / homology | Function and homology information ATP-dependent DNA damage sensor activity / ATP-dependent activity, acting on DNA / DNA recombination / damaged DNA binding / DNA repair / ATP hydrolysis activity / ATP binding Similarity search - Function | ||||||
Biological species | Methanococcus maripaludis (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.4 Å | ||||||
Authors | Li, Y. / He, Y. / Luo, Y. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2009 Title: Conservation of a conformational switch in RadA recombinase from Methanococcus maripaludis. Authors: Li, Y. / He, Y. / Luo, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3etl.cif.gz | 72.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3etl.ent.gz | 53.1 KB | Display | PDB format |
PDBx/mmJSON format | 3etl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/et/3etl ftp://data.pdbj.org/pub/pdb/validation_reports/et/3etl | HTTPS FTP |
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-Related structure data
Related structure data | 3ew9C 3ewaC 1t4gS 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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Details | Authors state that the quaternary structure is an infinite filament. Therefore, it is impossible to describe by a limited number of matrice. |
-Components
#1: Protein | Mass: 35205.168 Da / Num. of mol.: 1 / Mutation: I124M Source method: isolated from a genetically manipulated source Details: The radA open reading frame is inserted between the Nco I and Xho I sites Source: (gene. exp.) Methanococcus maripaludis (archaea) / Gene: MMP1222, radA / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Rosetta2 (DE3) / References: UniProt: Q977P5, UniProt: P0CW58*PLUS | ||
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#2: Chemical | ChemComp-ANP / | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.93 Å3/Da / Density % sol: 57.96 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.9 Details: 6-8% PEG 3350, 0.1 M NH4Cl, 0.05 M MgCl2, 0.05 M Tris-HCl, 1 mM AMPPNP, pH 7.9, VAPOR DIFFUSION, HANGING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 22, 2007 / Details: bending crystal |
Radiation | Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→20 Å / Num. all: 15781 / Num. obs: 15276 / % possible obs: 96.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.9 % / Rsym value: 0.069 / Net I/σ(I): 17.1 |
Reflection shell | Resolution: 2.4→2.5 Å / Redundancy: 9.3 % / Num. unique all: 1033 / Rsym value: 0.347 / % possible all: 72 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB entry 1T4G Resolution: 2.4→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.4→20 Å
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Refine LS restraints |
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