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Yorodumi- PDB-6gut: CRYSTAL STRUCTURE OF NON-TYPEABLE HAEMOPHILUS INFLUENZAE PROTEIN ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6gut | ||||||
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Title | CRYSTAL STRUCTURE OF NON-TYPEABLE HAEMOPHILUS INFLUENZAE PROTEIN E AND PILA EXPRESSED AS A SINGLE-CHAIN CHIMERIC PROTEIN | ||||||
Components | 23S rRNA pseudouridine synthase D,PilA | ||||||
Keywords | CELL ADHESION / BACTERIAL PROTEIN / SURFACE ADHESIN / PROT-E / PILA / SURFACE LIPOPROTEIN. / ADHESIN / PILIN / TYPE IV PILUS | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Haemophilus influenzae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 Å | ||||||
Authors | Somers, D. | ||||||
Citation | Journal: Infect.Immun. / Year: 2019 Title: Design and Characterization of Protein E-PilA, a Candidate Fusion Antigen for Nontypeable Haemophilus influenzae Vaccine. Authors: Blais, N. / Somers, D. / Faubert, D. / Labbe, S. / Castado, C. / Ysebaert, C. / Gagnon, L.P. / Champagne, J. / Gagne, M. / Martin, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6gut.cif.gz | 120.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6gut.ent.gz | 92 KB | Display | PDB format |
PDBx/mmJSON format | 6gut.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6gut_validation.pdf.gz | 463.5 KB | Display | wwPDB validaton report |
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Full document | 6gut_full_validation.pdf.gz | 465 KB | Display | |
Data in XML | 6gut_validation.xml.gz | 25.3 KB | Display | |
Data in CIF | 6gut_validation.cif.gz | 38.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gu/6gut ftp://data.pdbj.org/pub/pdb/validation_reports/gu/6gut | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 28753.170 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Haemophilus influenzae (bacteria) / Gene: rluD, CGSHi22121_05660, pilA / Production host: Escherichia coli (E. coli) / References: UniProt: A4MX90, UniProt: Q5D8E3 #2: Chemical | ChemComp-SO4 / #3: Chemical | #4: Chemical | ChemComp-GOL / | #5: 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: 2.69 Å3/Da / Density % sol: 54.28 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4 / Details: PEG4000, AMMONIUM SULPHATE, SODIUM ACETATE. |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97625 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 14, 2012 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.63→47.244 Å / Num. obs: 75506 / % possible obs: 99.5 % / Redundancy: 3.4 % / Biso Wilson estimate: 24.57 Å2 / Rpim(I) all: 0.039 / Rrim(I) all: 0.074 / Rsym value: 0.062 / Net I/av σ(I): 6.3 / Net I/σ(I): 10.4 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: IN-HOUSE Resolution: 1.63→20 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.959 / SU B: 1.728 / SU ML: 0.059 / SU R Cruickshank DPI: 0.0832 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.083 / ESU R Free: 0.085 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 101.24 Å2 / Biso mean: 24.587 Å2 / Biso min: 12.1 Å2
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Refinement step | Cycle: final / Resolution: 1.63→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.63→1.672 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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