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Yorodumi- PDB-5nqz: Structure of a fHbp(V1.1):PorA(P1.16) chimera. Fusion at fHbp pos... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5nqz | ||||||
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Title | Structure of a fHbp(V1.1):PorA(P1.16) chimera. Fusion at fHbp position 309. | ||||||
Components | Factor H binding protein,Major outer membrane protein P.IA,Factor H binding protein | ||||||
Keywords | IMMUNE SYSTEM / Meningitis / Vaccine / Complement / Chimeric | ||||||
Function / homology | Function and homology information bacterial extracellular vesicle / porin activity / pore complex / monoatomic ion transmembrane transport / cell outer membrane Similarity search - Function | ||||||
Biological species | Neisseria meningitidis MC58 (bacteria) Neisseria meningitidis serogroup C (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 Å | ||||||
Authors | Johnson, S. / Hollingshead, S. / Lea, S.M. / Tang, C.M. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Nat Commun / Year: 2018 Title: Structure-based design of chimeric antigens for multivalent protein vaccines. Authors: Hollingshead, S. / Jongerius, I. / Exley, R.M. / Johnson, S. / Lea, S.M. / Tang, C.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5nqz.cif.gz | 131.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5nqz.ent.gz | 100.3 KB | Display | PDB format |
PDBx/mmJSON format | 5nqz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5nqz_validation.pdf.gz | 465.1 KB | Display | wwPDB validaton report |
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Full document | 5nqz_full_validation.pdf.gz | 470.2 KB | Display | |
Data in XML | 5nqz_validation.xml.gz | 27.6 KB | Display | |
Data in CIF | 5nqz_validation.cif.gz | 41.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nq/5nqz ftp://data.pdbj.org/pub/pdb/validation_reports/nq/5nqz | HTTPS FTP |
-Related structure data
Related structure data | 5nqpC 5nqxC 5nqyC 4aydS 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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-Components
#1: Protein | Mass: 29127.508 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Neisseria meningitidis MC58, (gene. exp.) Neisseria meningitidis serogroup C (bacteria) Gene: NMB1870, porA / Variant: V1.1 / Plasmid: pET21b / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): B834 / References: UniProt: Q9JXV4, UniProt: P13415 #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-ACT / #4: Chemical | ChemComp-EDO / | #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: 2.49 Å3/Da / Density % sol: 51 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 5 Details: 0.01M zinc chloride, 0.1M sodium acetate, 20%(w/v) PEG6000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92818 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 4, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92818 Å / Relative weight: 1 |
Reflection | Resolution: 1.63→58.55 Å / Num. obs: 70772 / % possible obs: 98.6 % / Redundancy: 3 % / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.041 / Net I/σ(I): 12.7 |
Reflection shell | Resolution: 1.63→1.67 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.615 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 4967 / Rpim(I) all: 0.534 / % possible all: 93.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4ayd Resolution: 1.63→58.55 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.956 / SU B: 1.93 / SU ML: 0.063 / Cross valid method: THROUGHOUT / ESU R: 0.083 / ESU R Free: 0.085 / 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: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.699 Å2
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Refinement step | Cycle: 1 / Resolution: 1.63→58.55 Å
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Refine LS restraints |
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