+Open data
-Basic information
Entry | Database: PDB / ID: 3o2e | ||||||
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Title | Crystal structure of a bol-like protein from babesia bovis | ||||||
Components | BolA-like protein | ||||||
Keywords | UNKNOWN FUNCTION / SSGCID / Babesia bovis / iodide / SAD / Seattle Structural Genomics Center for Infectious Disease / BOL like protein | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Babesia bovis (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SAD / Resolution: 1.95 Å | ||||||
Authors | Seattle Structural Genomics Center for Infectious Disease (SSGCID) | ||||||
Citation | Journal: J.Struct.Funct.Genom. / Year: 2011 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3o2e.cif.gz | 49.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3o2e.ent.gz | 34.1 KB | Display | PDB format |
PDBx/mmJSON format | 3o2e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o2/3o2e ftp://data.pdbj.org/pub/pdb/validation_reports/o2/3o2e | HTTPS FTP |
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-Related structure data
Related structure data | 3k9gC 3km3C 3kw3C 3luzC 3menC 3njbC 3oibC 3p96C 3pfdC 3pm6C C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-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.) Babesia bovis (eukaryote) / Strain: T2BO / Gene: GeneID:5478071 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A7ATL3 | ||||
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#2: Chemical | ChemComp-IOD / #3: Chemical | ChemComp-MG / | #4: 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: 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: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 / Wavelength: 1.5418 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: SAD 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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