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Yorodumi- PDB-2evv: Crystal Structure of the PEBP-like Protein of Unknown Function HP... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2evv | ||||||
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Title | Crystal Structure of the PEBP-like Protein of Unknown Function HP0218 from Helicobacter pylori | ||||||
Components | hypothetical protein HP0218 | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / alpha-beta structure / dimer / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | YbhB/YbcL / Phosphatidylethanolamine-binding Protein / PEBP-like / Phosphatidylethanolamine-binding protein / Phosphatidylethanolamine-binding protein / PEBP-like superfamily / Alpha-Beta Complex / Alpha Beta / Uncharacterized protein Function and homology information | ||||||
Biological species | Helicobacter pylori (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.59 Å | ||||||
Authors | Kim, Y. / Xu, X. / Hong, H. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: Crystal Structure of the Hypothetical Protein HP0218 from Helicobacter pylori Authors: Kim, Y. / Xu, X. / Hong, H. / Savchenko, A. / Edwards, A. / Joachimiak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2evv.cif.gz | 161 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2evv.ent.gz | 135.7 KB | Display | PDB format |
PDBx/mmJSON format | 2evv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2evv_validation.pdf.gz | 484.1 KB | Display | wwPDB validaton report |
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Full document | 2evv_full_validation.pdf.gz | 502.8 KB | Display | |
Data in XML | 2evv_validation.xml.gz | 32.1 KB | Display | |
Data in CIF | 2evv_validation.cif.gz | 44.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ev/2evv ftp://data.pdbj.org/pub/pdb/validation_reports/ev/2evv | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 23806.879 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: 26695 / Gene: HP0218 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: O25006 #2: Chemical | ChemComp-GOL / #3: Chemical | ChemComp-SO4 / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.93 Å3/Da / Density % sol: 68.68 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 0.1M Bis-Tris PH6.0, 0.2M Ammonium Sulphate, 20%PEG4K, 2% Glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97922 Å |
Detector | Type: SBC-3 / Detector: CCD / Date: Apr 3, 2005 / Details: mirrors |
Radiation | Monochromator: double crystal monochromator, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97922 Å / Relative weight: 1 |
Reflection | Resolution: 2.59→45.75 Å / Num. all: 48287 / Num. obs: 47122 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.1 % / Rmerge(I) obs: 0.191 / Net I/σ(I): 4.9 |
Reflection shell | Resolution: 2.59→2.68 Å / Redundancy: 8.6 % / Rmerge(I) obs: 0.798 / Mean I/σ(I) obs: 2.2 / Num. unique all: 3786 / % possible all: 79.7 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.59→45.75 Å / Cor.coef. Fo:Fc: 0.905 / Cor.coef. Fo:Fc free: 0.871 / SU B: 16.496 / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.366 / ESU R Free: 0.276 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. CNS 1.1 was also used in refinement.
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.218 Å2
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Refinement step | Cycle: LAST / Resolution: 2.59→45.75 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.592→2.66 Å / Total num. of bins used: 20
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