+Open data
-Basic information
Entry | Database: PDB / ID: 2zrj | ||||||
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Title | MsRecA Q196A ATPgS form IV | ||||||
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: 2.6 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 | 2zrj.cif.gz | 77 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2zrj.ent.gz | 55.4 KB | Display | PDB format |
PDBx/mmJSON format | 2zrj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2zrj_validation.pdf.gz | 996.9 KB | Display | wwPDB validaton report |
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Full document | 2zrj_full_validation.pdf.gz | 1008.6 KB | Display | |
Data in XML | 2zrj_validation.xml.gz | 16.3 KB | Display | |
Data in CIF | 2zrj_validation.cif.gz | 21.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zr/2zrj ftp://data.pdbj.org/pub/pdb/validation_reports/zr/2zrj | HTTPS FTP |
-Related structure data
Related structure data | 2zr0C 2zr7C 2zr9C 2zraC 2zrbC 2zrcC 2zrdC 2zreC 2zrfC 2zrgC 2zrhC 2zriC 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 37287.441 Da / Num. of mol.: 1 / Mutation: Q196A 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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-Non-polymers , 5 types, 68 molecules
#2: Chemical | ChemComp-AGS / | ||||
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#3: Chemical | ChemComp-CL / | ||||
#4: Chemical | #5: Chemical | ChemComp-PE4 / | #6: 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: 3.03 Å3/Da / Density % sol: 59.38 % |
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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 21, 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: 2.6→30 Å / Num. all: 13807 / Num. obs: 13807 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Biso Wilson estimate: 52.3 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 18.5 |
Reflection shell | Resolution: 2.6→2.74 Å / Redundancy: 4 % / Rmerge(I) obs: 0.371 / Mean I/σ(I) obs: 3 / Num. unique all: 1995 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1UBC Resolution: 2.6→24.97 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1326391.39 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / 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: 59.8464 Å2 / ksol: 0.35 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 57.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.6→24.97 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.76 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
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Xplor file |
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