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Yorodumi- PDB-5j4g: Crystal structure of the C-terminally His6-tagged HP0902, an unch... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5j4g | ||||||
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Title | Crystal structure of the C-terminally His6-tagged HP0902, an uncharacterized protein from Helicobacter pylori 26695 | ||||||
Components | Uncharacterized protein | ||||||
Keywords | UNKNOWN FUNCTION / HP0902 / Helicobacter pylori / secretory protein / Cupin family / Uncharacterized protein | ||||||
Function / homology | RmlC-like cupin domain superfamily / RmlC-like jelly roll fold / Cupin domain-containing protein Function and homology information | ||||||
Biological species | Helicobacter pylori (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Sim, D.W. / Lee, W.C. / Kim, H.Y. / Kim, J.H. / Won, H.S. | ||||||
Citation | Journal: FEBS Lett. / Year: 2016 Title: Structural identification of the lipopolysaccharide-binding capability of a cupin-family protein from Helicobacter pylori Authors: Sim, D.W. / Kim, J.H. / Kim, H.Y. / Jang, J.H. / Lee, W.C. / Kim, E.H. / Park, P.J. / Lee, K.H. / Won, H.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5j4g.cif.gz | 50.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5j4g.ent.gz | 35.8 KB | Display | PDB format |
PDBx/mmJSON format | 5j4g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5j4g_validation.pdf.gz | 432.4 KB | Display | wwPDB validaton report |
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Full document | 5j4g_full_validation.pdf.gz | 433.7 KB | Display | |
Data in XML | 5j4g_validation.xml.gz | 9.3 KB | Display | |
Data in CIF | 5j4g_validation.cif.gz | 12.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j4/5j4g ftp://data.pdbj.org/pub/pdb/validation_reports/j4/5j4g | HTTPS FTP |
-Related structure data
Related structure data | 5j4fC 2q30S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 12119.166 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: C-terminal 6xHis tag Source: (gene. exp.) Helicobacter pylori (strain ATCC 700392 / 26695) (bacteria) Strain: ATCC 700392 / 26695 / Gene: HP_0902 / Production host: Escherichia coli (E. coli) / References: UniProt: O25562 #2: 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: 1.86 Å3/Da / Density % sol: 33.77 % / Description: short needle |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: PEG 3350, ammonium acetate, bis-tris |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 0.98 Å |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Dec 12, 2010 |
Radiation | Monochromator: Cryo-cooled channel-cut Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→71 Å / Num. obs: 6158 / % possible obs: 98.2 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.042 / Net I/σ(I): 39.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2q30 Resolution: 2.6→41.076 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 0.03 / Phase error: 11.76 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→41.076 Å
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Refine LS restraints |
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LS refinement shell |
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