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Yorodumi- PDB-3a5u: Promiscuity and specificity in DNA binding to SSB: Insights from ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3a5u | ||||||
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Title | Promiscuity and specificity in DNA binding to SSB: Insights from the structure of the Mycobacterium smegmatis SSB-ssDNA complex | ||||||
Components |
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Keywords | DNA BINDING PROTEIN / DNA damage / DNA repair / DNA replication / DNA-binding | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Mycobacterium smegmatis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Kaushal, P.S. / Manjunath, G.P. / Sekar, K. / Muniyappa, K. / Vijayan, M. | ||||||
Citation | Journal: To be Published / Year: 2009 Title: Promiscuity and specificity in DNA binding to SSB: Insights from the structure of the Mycobacterium smegmatis SSB-ssDNA complex. Authors: Kaushal, P.S. / Manjunath, G.P. / Sekar, K. / Muniyappa, K. / Vijayan, M. #1: Journal: Nat.Struct.Biol. / Year: 2000 Title: Structure of the DNA binding domain of E. coli SSB bound to ssDNA Authors: Raghunathan, S. / Kozlov, A.G. / Lohman, T.M. / Waksman, G. #2: Journal: J.Mol.Biol. / Year: 2003 Title: Structure of Mycobacterium tuberculosis single-stranded DNA-binding protein. Variability in quaternary structure and its implications Authors: Saikrishnan, K. / Jeyakanthan, J. / Venkatesh, J. / Acharya, N. / Sekar, K. / Varshney, U. / Vijayan, M. #3: Journal: Acta Crystallogr.,Sect.D / Year: 2005 Title: Structure of Mycobacterium smegmatis single-stranded DNA-binding protein and a comparative study involving homologus SSBs: biological implications of structural plasticity and variability in quaternary association Authors: Saikrishnan, K. / Manjunath, G.P. / Singh, P. / Jeyakanthan, J. / Dauter, Z. / Sekar, K. / Muniyappa, K. / Vijayan, M. #4: Journal: J.Mol.Biol. / Year: 2009 Title: Single-stranded DNA-binding protein complex from Helicobacter pylori suggests an ssDNA-binding surface Authors: Chan, K.W. / Lee, Y.J. / Wang, C.H. / Huang, H. / Sun, Y.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3a5u.cif.gz | 126.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3a5u.ent.gz | 98.4 KB | Display | PDB format |
PDBx/mmJSON format | 3a5u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3a5u_validation.pdf.gz | 445.6 KB | Display | wwPDB validaton report |
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Full document | 3a5u_full_validation.pdf.gz | 462.5 KB | Display | |
Data in XML | 3a5u_validation.xml.gz | 14.1 KB | Display | |
Data in CIF | 3a5u_validation.cif.gz | 18.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a5/3a5u ftp://data.pdbj.org/pub/pdb/validation_reports/a5/3a5u | HTTPS FTP |
-Related structure data
Related structure data | 1x3eS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: 1 / Refine code: 2
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-Components
#1: Protein | Mass: 14042.684 Da / Num. of mol.: 2 / Fragment: Chymotryptic fragment, UNP residues 1-130 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium smegmatis (bacteria) / Strain: mc(2)155 / Gene: ssb / Plasmid: PET17B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q9AFI5 #2: DNA chain | | Mass: 8919.677 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Biomolecule has been synthesized #3: 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: 2.07 Å3/Da / Density % sol: 40.49 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 100mM Hepes, pH7.5, 30% PEG200, 22% PEG4000, 10% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 19, 2009 |
Radiation | Monochromator: OSMIC MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→30 Å / Num. all: 8062 / Num. obs: 8048 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Biso Wilson estimate: 76 Å2 / Rsym value: 0.101 / Net I/σ(I): 15.8 |
Reflection shell | Resolution: 2.8→2.95 Å / Redundancy: 5.4 % / Mean I/σ(I) obs: 2.7 / Num. unique all: 1135 / Rsym value: 0.543 / % possible all: 99.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1X3E Resolution: 2.8→30 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.87 / SU B: 26.401 / SU ML: 0.274 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R Free: 0.436 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 65.384 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→30 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.8→2.872 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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