+Open data
-Basic information
Entry | Database: PDB / ID: 3t9j | ||||||
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Title | Crystal structure HP-NAP from strain YS39 in apo form | ||||||
Components | Neutrophil-activating protein | ||||||
Keywords | METAL TRANSPORT / DODECAMER / FOUR-HELIX BUNDLE | ||||||
Function / homology | Function and homology information oxidoreductase activity, acting on metal ions / ferric iron binding / cytoplasm Similarity search - Function | ||||||
Biological species | Helicobacter pylori (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Tsuruta, O. / Yokoyama, H. / Fujii, S. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2012 Title: A new crystal lattice structure of Helicobacter pylori neutrophil-activating protein (HP-NAP) Authors: Tsuruta, O. / Yokoyama, H. / Fujii, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3t9j.cif.gz | 44.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3t9j.ent.gz | 32.5 KB | Display | PDB format |
PDBx/mmJSON format | 3t9j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3t9j_validation.pdf.gz | 441.8 KB | Display | wwPDB validaton report |
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Full document | 3t9j_full_validation.pdf.gz | 442.1 KB | Display | |
Data in XML | 3t9j_validation.xml.gz | 8.4 KB | Display | |
Data in CIF | 3t9j_validation.cif.gz | 11 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t9/3t9j ftp://data.pdbj.org/pub/pdb/validation_reports/t9/3t9j | HTTPS FTP |
-Related structure data
Related structure data | 3ta8C 1ji4S 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 19006.621 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: YS39 / Gene: napA / Plasmid: pET-15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: G1UIZ3 |
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#2: Chemical | ChemComp-EDO / |
#3: 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: 3.73 Å3/Da / Density % sol: 67 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.8 Details: 0.1M L-arginine, 20% ethylene glycol, pH 8.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Mar 1, 2010 / Details: mirror |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→20 Å / Num. obs: 15374 / % possible obs: 99.9 % / Redundancy: 13.5 % / Biso Wilson estimate: 38.9 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 66.4 |
Reflection shell | Resolution: 2.2→2.24 Å / Rmerge(I) obs: 0.365 / Mean I/σ(I) obs: 11.2 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1JI4 Resolution: 2.2→19.34 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.921 / SU B: 4.358 / SU ML: 0.114 / Cross valid method: THROUGHOUT / ESU R Free: 0.166 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.041 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→19.34 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.203→2.26 Å / Total num. of bins used: 20
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