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Yorodumi- PDB-5j4f: Crystal structure of the N-terminally His6-tagged HP0902, an unch... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5j4f | ||||||
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Title | Crystal structure of the N-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: 1.4 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 | 5j4f.cif.gz | 55.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5j4f.ent.gz | 38.5 KB | Display | PDB format |
PDBx/mmJSON format | 5j4f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5j4f_validation.pdf.gz | 443.4 KB | Display | wwPDB validaton report |
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Full document | 5j4f_full_validation.pdf.gz | 445.3 KB | Display | |
Data in XML | 5j4f_validation.xml.gz | 11.7 KB | Display | |
Data in CIF | 5j4f_validation.cif.gz | 16.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j4/5j4f ftp://data.pdbj.org/pub/pdb/validation_reports/j4/5j4f | HTTPS FTP |
-Related structure data
Related structure data | 5j4gC 2q30S S: Starting model for refinement C: citing same article (ref.) |
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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: 13219.380 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source 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: 1.91 Å3/Da / Density % sol: 35.61 % / Description: short needle |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: PEG 3350, sodium chloride, Tris-HCl |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 12, 2010 |
Radiation | Monochromator: Numerical link type Si(111) double crystal monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→71 Å / Num. obs: 38998 / % possible obs: 99.8 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 15.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2q30 Resolution: 1.4→19.85 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.962 / SU B: 1.102 / SU ML: 0.044 / Cross valid method: FREE R-VALUE / ESU R: 0.061 / ESU R Free: 0.063 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.028 Å2
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Refinement step | Cycle: LAST / Resolution: 1.4→19.85 Å
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Refine LS restraints |
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