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- PDB-3dm8: Crystal Structure of Putative Isomerase from Rhodopseudomonas pal... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3dm8 | ||||||
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Title | Crystal Structure of Putative Isomerase from Rhodopseudomonas palustris | ||||||
![]() | uncharacterized protein RPA4348 | ||||||
![]() | structural genomics / unknown function / SIRAS / Putative Isomerase / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | SnoaL-like domain / SnoaL-like domain / Nuclear Transport Factor 2; Chain: A, - #50 / NTF2-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta / DODECYL NONA ETHYLENE GLYCOL ETHER / SnoaL-like domain-containing protein![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Cymborowski, M. / Chruszcz, M. / Skarina, T. / Kagan, O. / Savchenko, A. / Edwards, A.M. / Joachimiak, A. / Minor, W. / Midwest Center for Structural Genomics (MCSG) | ||||||
![]() | ![]() Title: Crystal Structure of Putative Isomerase from Rhodopseudomonas palustris Authors: Cymborowski, M. / Minor, W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 46.4 KB | Display | ![]() |
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PDB format | ![]() | 31.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 643.1 KB | Display | ![]() |
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Full document | ![]() | 643 KB | Display | |
Data in XML | ![]() | 9.5 KB | Display | |
Data in CIF | ![]() | 13.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 16360.834 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: RPA4348 / Plasmid: P15TV LIC / Production host: ![]() ![]() |
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#2: Chemical | ChemComp-CE9 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 51.46 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion / pH: 7.5 Details: PEG400 15%, MgCl2 0.2M, 0.1M Hepes, pH 7.5, VAPOR DIFFUSION, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: APS-1 / Detector: CCD / Date: Feb 8, 2007 / Details: MIRROR |
Radiation | Monochromator: SI-111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97912 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→48.62 Å / Num. all: 15870 / Num. obs: 15870 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 7.5 % / Rmerge(I) obs: 0.057 / Rsym value: 0.057 / Net I/σ(I): 35 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.322 / Mean I/σ(I) obs: 6.2 / Rsym value: 0.322 / % possible all: 96.3 |
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Processing
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Refinement | Method to determine structure: SIR/SIRAS / Resolution: 1.8→48.62 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.935 / SU B: 4.219 / SU ML: 0.072 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.117 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.62 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→48.62 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.84 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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