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Open data
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Basic information
Entry | Database: PDB / ID: 3o2e | ||||||
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Title | Crystal structure of a bol-like protein from babesia bovis | ||||||
![]() | BolA-like protein | ||||||
![]() | UNKNOWN FUNCTION / SSGCID / Babesia bovis / iodide / SAD / Seattle Structural Genomics Center for Infectious Disease / BOL like protein | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Seattle Structural Genomics Center for Infectious Disease (SSGCID) | ||||||
![]() | ![]() Title: SAD phasing using iodide ions in a high-throughput structural genomics environment. Authors: Abendroth, J. / Gardberg, A.S. / Robinson, J.I. / Christensen, J.S. / Staker, B.L. / Myler, P.J. / Stewart, L.J. / Edwards, T.E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 49.1 KB | Display | ![]() |
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PDB format | ![]() | 34.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 425.3 KB | Display | ![]() |
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Full document | ![]() | 425.2 KB | Display | |
Data in XML | ![]() | 6.2 KB | Display | |
Data in CIF | ![]() | 7.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3k9gC ![]() 3km3C ![]() 3kw3C ![]() 3luzC ![]() 3menC ![]() 3njbC ![]() 3oibC ![]() 3p96C ![]() 3pfdC ![]() 3pm6C C: citing same article ( |
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Similar structure data | |
Other databases |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 11601.238 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||
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#2: Chemical | ChemComp-IOD / #3: Chemical | ChemComp-MG / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.64 Å3/Da / Density % sol: 25 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: EBS JCSG SCREEN E2: 2M AMMONIUM SULPHATE, 100MM CACODYLATE PH 6.5, 200MM NACL: BABOA.10365.A AT 12.4MG/ML, ENCUA.00735 AT 29.3MG/ML, PH N/A, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: May 20, 2009 / Details: Rigaku/Osmic VariMax HF |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→20 Å / Num. obs: 6133 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 18.3 % / Biso Wilson estimate: 25.8 Å2 / Rmerge(I) obs: 0.094 / Net I/σ(I): 19.39 |
Reflection shell | Resolution: 1.95→2 Å / Redundancy: 7 % / Rmerge(I) obs: 0.481 / Mean I/σ(I) obs: 4.4 / Num. unique all: 795 / % possible all: 99.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: iodide SAD Resolution: 1.95→19.53 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.908 / SU B: 6.861 / SU ML: 0.108 / Isotropic thermal model: isotropic, TLS / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.167 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE
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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: 15.51 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→19.53 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 15.521 Å / Origin y: 30.589 Å / Origin z: 2.283 Å
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