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Yorodumi- PDB-2bo3: Crystal Structure of HP0242, a Hypothetical Protein from Helicoba... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2bo3 | ||||||
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Title | Crystal Structure of HP0242, a Hypothetical Protein from Helicobacter pylori | ||||||
Components | HYPOTHETICAL PROTEIN HP0242 | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / HELICOBACTER PYLORI / HYPOTHETICAL PROTEIN | ||||||
Function / homology | HP0242-like domain / HP0242-like fold / Protein of unknown function DUF2018 / HP0242-like superfamily / Domain of unknown function (DUF2018) / Orthogonal Bundle / Mainly Alpha / metal ion binding / DUF2018 family protein Function and homology information | ||||||
Biological species | HELICOBACTER PYLORI (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.27 Å | ||||||
Authors | Sun, Y.-J. / Tsai, J.-Y. / Chen, B.-T. | ||||||
Citation | Journal: Proteins: Struct., Funct., Bioinf. / Year: 2006 Title: Crystal Structure of Hp0242, a Hypothetical Protein from Helicobacter Pylori with a Novel Fold Authors: Tsai, J.-Y. / Chen H, B.-T. / Cheng, C. / Chen, H.Y. / Hsiao, N.W. / Liu, P.C. / Sun, Y.-J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2bo3.cif.gz | 30.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2bo3.ent.gz | 20.9 KB | Display | PDB format |
PDBx/mmJSON format | 2bo3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2bo3_validation.pdf.gz | 428.6 KB | Display | wwPDB validaton report |
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Full document | 2bo3_full_validation.pdf.gz | 432.5 KB | Display | |
Data in XML | 2bo3_validation.xml.gz | 6.5 KB | Display | |
Data in CIF | 2bo3_validation.cif.gz | 8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bo/2bo3 ftp://data.pdbj.org/pub/pdb/validation_reports/bo/2bo3 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | REMARK: THE PROTEIN HAS A NOVEL FOLDING AND THE DIMERMIMICS A TIGHT FIGURE-OF-EIGHT KNOT STRUCTURE |
-Components
#1: Protein | Mass: 11101.640 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HELICOBACTER PYLORI (bacteria) / Plasmid: PET30A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834(DE3) / References: UniProt: O25025 |
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#2: 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: 2.62 Å3/Da / Density % sol: 53 % |
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Crystal grow | pH: 8.5 / Details: pH 8.50 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL12B2 / Wavelength: 0.9799 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Dec 7, 2004 |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9799 Å / Relative weight: 1 |
Reflection | Resolution: 2.27→27.72 Å / Num. obs: 5957 / % possible obs: 93.6 % / Observed criterion σ(I): 2 / Redundancy: 11.9 % / Biso Wilson estimate: 20.7 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 37.2 |
Reflection shell | Resolution: 2.27→2.35 Å / Redundancy: 11.8 % / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 11.9 / % possible all: 92.4 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.27→27.72 Å / Rfactor Rfree error: 0.013 / Data cutoff high absF: 311185.28 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 46.9536 Å2 / ksol: 0.369059 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 48.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.27→27.72 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.34 Å / Rfactor Rfree error: 0.053 / Total num. of bins used: 6
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Xplor file |
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