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Yorodumi- PDB-3maj: Crystal structure of putative DNA processing protein DprA from Rh... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3maj | ||||||
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Title | Crystal structure of putative DNA processing protein DprA from Rhodopseudomonas palustris CGA009 | ||||||
Components | DNA processing chain A | ||||||
Keywords | DNA BINDING PROTEIN / MCSG / PSI-2 / Structural Genomics / Protein Structure Initiative / Midwest Center for Structural Genomics / DNA processing protein DprA | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Rhodopseudomonas palustris (phototrophic) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.05 Å | ||||||
Authors | Chang, C. / Xu, X. / Cui, H. / Chin, S. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: Crystal structure of putative DNA processing protein DprA from Rhodopseudomonas palustris Authors: Chang, C. / Xu, X. / Cui, H. / Chin, S. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3maj.cif.gz | 78 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3maj.ent.gz | 61.9 KB | Display | PDB format |
PDBx/mmJSON format | 3maj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3maj_validation.pdf.gz | 436.3 KB | Display | wwPDB validaton report |
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Full document | 3maj_full_validation.pdf.gz | 438 KB | Display | |
Data in XML | 3maj_validation.xml.gz | 15.3 KB | Display | |
Data in CIF | 3maj_validation.cif.gz | 21.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ma/3maj ftp://data.pdbj.org/pub/pdb/validation_reports/ma/3maj | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 40330.008 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodopseudomonas palustris (phototrophic) Gene: DprA, RPA3120 / Plasmid: pET derivative / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)gold / References: UniProt: Q6N563 | ||
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#2: Chemical | #3: 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: 2.23 Å3/Da / Density % sol: 44.93 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.1 M Tris-Cl, 1.5 M Ammonium sulfate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 297K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97937 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 8, 2010 |
Radiation | Monochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97937 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→50 Å / Num. all: 23364 / Num. obs: 23262 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 7.1 % / Biso Wilson estimate: 35.3 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 42.5 |
Reflection shell | Resolution: 2.05→2.09 Å / Redundancy: 7 % / Rmerge(I) obs: 0.691 / Mean I/σ(I) obs: 4.23 / Num. unique all: 1131 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.05→43.77 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.932 / SU B: 9.247 / SU ML: 0.114 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.197 / ESU R Free: 0.174 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.824 Å2
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Refinement step | Cycle: LAST / Resolution: 2.05→43.77 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.05→2.105 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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