+Open data
-Basic information
Entry | Database: PDB / ID: 2zra | ||||||
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Title | MsRecA Q196E ATPgS | ||||||
Components | Protein recA | ||||||
Keywords | HYDROLASE / recombination / RecA mutants / DNA-REPAIR / ATP-binding / DNA damage / DNA recombination / DNA repair / DNA-binding / Nucleotide-binding / SOS response | ||||||
Function / homology | Function and homology information ATP-dependent DNA damage sensor activity / SOS response / single-stranded DNA binding / DNA recombination / damaged DNA binding / DNA repair / ATP hydrolysis activity / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | Mycobacterium smegmatis str. MC2 155 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.1 Å | ||||||
Authors | Prabu, J.R. / Manjunath, G.P. / Chandra, N.R. / Muniyappa, K. / Vijayan, M. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2008 Title: Functionally important movements in RecA molecules and filaments: studies involving mutation and environmental changes Authors: Prabu, J.R. / Manjunath, G.P. / Chandra, N.R. / Muniyappa, K. / Vijayan, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2zra.cif.gz | 69.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2zra.ent.gz | 50.3 KB | Display | PDB format |
PDBx/mmJSON format | 2zra.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2zra_validation.pdf.gz | 796 KB | Display | wwPDB validaton report |
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Full document | 2zra_full_validation.pdf.gz | 807.2 KB | Display | |
Data in XML | 2zra_validation.xml.gz | 15.9 KB | Display | |
Data in CIF | 2zra_validation.cif.gz | 20.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zr/2zra ftp://data.pdbj.org/pub/pdb/validation_reports/zr/2zra | HTTPS FTP |
-Related structure data
Related structure data | 2zr0C 2zr7C 2zr9C 2zrbC 2zrcC 2zrdC 2zreC 2zrfC 2zrgC 2zrhC 2zriC 2zrjC 2zrkC 2zrlC 2zrmC 2zrnC 2zroC 2zrpC 1ubcS 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: 37345.473 Da / Num. of mol.: 1 / Mutation: Q196E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium smegmatis str. MC2 155 (bacteria) Plasmid: PTHIOA / Production host: Escherichia coli (E. coli) / Strain (production host): JC10289 / References: UniProt: Q59560, EC: 3.4.99.37 | ||||
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#2: Chemical | ChemComp-AGS / | ||||
#3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-CL / | #5: 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: 3.24 Å3/Da / Density % sol: 61.98 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 6.9 Details: 80mM citrate/phosphate buffer(pH 6.9), 80mM NaCl, 40mM ammonium acetate, 20mM sodium citrate, 6% poly-ethylene glycol 3350, 30% poly-ethylene glycol 3350, 200mM ammonium acetate in sodium ...Details: 80mM citrate/phosphate buffer(pH 6.9), 80mM NaCl, 40mM ammonium acetate, 20mM sodium citrate, 6% poly-ethylene glycol 3350, 30% poly-ethylene glycol 3350, 200mM ammonium acetate in sodium citrate buffer(PH 5.8) , VAPOR DIFFUSION, HANGING DROP, temperature 296K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 20, 2006 / Details: Mirrors |
Radiation | Monochromator: Single crystal, cylindrically bent, Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→30 Å / Num. obs: 8701 / % possible obs: 99.2 % / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Rmerge(I) obs: 0.116 / Net I/σ(I): 13 |
Reflection shell | Resolution: 3.1→3.27 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.452 / Mean I/σ(I) obs: 3 / Num. unique all: 1265 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1UBC Resolution: 3.1→28.68 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 1259427.84 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 63.463 Å2 / ksol: 0.35 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 58.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.1→28.68 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.1→3.29 Å / Rfactor Rfree error: 0.035 / Total num. of bins used: 6
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Xplor file |
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