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- PDB-3o0y: The crystal structure of the putative lipoprotein from Colwellia ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3o0y | ||||||
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Title | The crystal structure of the putative lipoprotein from Colwellia psychrerythraea | ||||||
![]() | lipoprotein | ||||||
![]() | LIPID BINDING PROTEIN / Structural genomics / PSI2 / MCSG / Protein Structure Initiative / Midwest Center for Structural Genomics / lipoprotein | ||||||
Function / homology | Protein of unknown function DUF885 / Bacterial protein of unknown function (DUF885) / Putative lipoprotein![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zhang, R. / Chhor, G. / Cobb, G. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
![]() | ![]() Title: The crystal structure of the putative lipoprotein from Colwellia psychrerythraea Authors: Zhang, R. / Chhor, G. / Cobb, G. / Joachimiak, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 403.9 KB | Display | ![]() |
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PDB format | ![]() | 325.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 489.4 KB | Display | ![]() |
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Full document | ![]() | 517.2 KB | Display | |
Data in XML | ![]() | 88 KB | Display | |
Data in CIF | ![]() | 137.8 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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2 | ![]()
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3 | ![]()
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4 |
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Unit cell |
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Details | It looks like the molecules A,B,C form the trimer in the solution. |
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Components
#1: Protein | Mass: 68047.602 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-SO4 / #3: Chemical | #4: Chemical | ChemComp-GOL / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.63 Å3/Da / Density % sol: 53.26 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.2M Lithium sulfate monohydrate, 0.1M Bis-tris pH5.5, 25% PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 21, 2009 / Details: mirrors | |||||||||
Radiation | Monochromator: Si 111 channel / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 1.7→85.13 Å / Num. all: 216434 / Num. obs: 206348 / % possible obs: 95.34 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 1.4 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 9.85 | |||||||||
Reflection shell | Resolution: 1.703→1.747 Å / Redundancy: 1.2 % / Rmerge(I) obs: 0.623 / Mean I/σ(I) obs: 1 / Num. unique all: 16813 / % possible all: 72.08 |
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Processing
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Refinement | Method to determine structure: ![]() 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: 11.486 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→85.13 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.703→1.747 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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