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Yorodumi- PDB-4b7o: THE FrpB IRON TRANSPORTER FROM NEISSERIA MENINGITIDIS (F5-1 VARIA... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4b7o | ||||||
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Title | THE FrpB IRON TRANSPORTER FROM NEISSERIA MENINGITIDIS (F5-1 VARIANT) APOPROTEIN FORM | ||||||
Components | IRON-REGULATED OUTER MEMBRANE PROTEIN | ||||||
Keywords | TRANSPORT PROTEIN / TONB-DEPENDENT TRANSPORTER | ||||||
Function / homology | Function and homology information siderophore uptake transmembrane transporter activity / cell outer membrane / signaling receptor activity Similarity search - Function | ||||||
Biological species | NEISSERIA MENINGITIDIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.32 Å | ||||||
Authors | Saleem, M. / Prince, S.M. / Derrick, J.P. | ||||||
Citation | Journal: Plos One / Year: 2013 Title: Use of a Molecular Decoy to Segregate Transport from Antigenicity in the Frpb Iron Transporter from Neisseria Meningitidis. Authors: Saleem, M. / Prince, S.M. / Rigby, S.E.J. / Imran, M. / Patel, H. / Chan, H. / Sanders, H. / Maiden, M.C.J. / Feavers, I.M. / Derrick, J.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4b7o.cif.gz | 140.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4b7o.ent.gz | 108.8 KB | Display | PDB format |
PDBx/mmJSON format | 4b7o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4b7o_validation.pdf.gz | 441.5 KB | Display | wwPDB validaton report |
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Full document | 4b7o_full_validation.pdf.gz | 462 KB | Display | |
Data in XML | 4b7o_validation.xml.gz | 26.4 KB | Display | |
Data in CIF | 4b7o_validation.cif.gz | 36.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b7/4b7o ftp://data.pdbj.org/pub/pdb/validation_reports/b7/4b7o | HTTPS FTP |
-Related structure data
Related structure data | 4aipC 4aiqSC 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: 82710.898 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) NEISSERIA MENINGITIDIS (bacteria) / Variant: F5-1 / Plasmid: PET30EKLIC / Production host: ESCHERICHIA COLI B (bacteria) / Variant (production host): T7 EXPRESS / References: UniProt: Q841A2 |
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#2: Water | ChemComp-HOH / |
Sequence details | SEQUENCE CONFLICTS DUE TO STRAIN VARIATION |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.1 Å3/Da / Density % sol: 61 % / Description: NONE |
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Crystal grow | Details: 20MM NA L-GLUTAMATE, 20MM D, L-ALANINE, 20MM GLYCINE, 20MM LYSINE (RACEMIC), 20MM SERINE (RACEMIC), 39.8MM IMIDAZOLE, 24% (W/V) PEGMME550, 12% (W/V) PEG 20,000 AND 61.2MM MES/NAOH (PH 6.5) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.969 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Aug 11, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.969 Å / Relative weight: 1 |
Reflection | Resolution: 2.32→37 Å / Num. obs: 43114 / % possible obs: 98.2 % / Observed criterion σ(I): 2 / Redundancy: 2.2 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 9.8 |
Reflection shell | Resolution: 2.32→2.38 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 2 / % possible all: 98.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4AIQ Resolution: 2.32→37.05 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.907 / SU B: 8.223 / SU ML: 0.193 / Cross valid method: THROUGHOUT / ESU R: 0.281 / ESU R Free: 0.237 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.092 Å2
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Refinement step | Cycle: LAST / Resolution: 2.32→37.05 Å
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Refine LS restraints |
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