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Yorodumi- PDB-5t5f: Neisseria meningitidis factor H binding protein in complex with m... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5t5f | ||||||
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Title | Neisseria meningitidis factor H binding protein in complex with monoclonal antibody JAR5 | ||||||
Components |
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Keywords | PROTEIN BINDING / fHbp / JAR5 / epitope mapping / monoclonal antibody / cooperativity / Neisseria meningitidis | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Neisseria meningitidis (bacteria) Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.98 Å | ||||||
Authors | Malito, E. | ||||||
Citation | Journal: Biochem. J. / Year: 2016 Title: Neisseria meningitidis factor H-binding protein bound to monoclonal antibody JAR5: implications for antibody synergy. Authors: Malito, E. / Lo Surdo, P. / Veggi, D. / Santini, L. / Stefek, H. / Brunelli, B. / Luzzi, E. / Bottomley, M.J. / Beernink, P.T. / Scarselli, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5t5f.cif.gz | 139.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5t5f.ent.gz | 107 KB | Display | PDB format |
PDBx/mmJSON format | 5t5f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5t5f_validation.pdf.gz | 446.8 KB | Display | wwPDB validaton report |
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Full document | 5t5f_full_validation.pdf.gz | 459.6 KB | Display | |
Data in XML | 5t5f_validation.xml.gz | 24.6 KB | Display | |
Data in CIF | 5t5f_validation.cif.gz | 33.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t5/5t5f ftp://data.pdbj.org/pub/pdb/validation_reports/t5/5t5f | HTTPS FTP |
-Related structure data
Related structure data | 2w80S S: Starting model for refinement |
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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: 26838.957 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Neisseria meningitidis (bacteria) / Gene: fhbp Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: Q6VRZ6, UniProt: Q9JXV4*PLUS |
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#2: Antibody | Mass: 23204.207 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) |
#3: Antibody | Mass: 23865.557 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) |
#4: 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: 3.57 Å3/Da / Density % sol: 65.2 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 5 Details: 20% Polyethylene glycol (PEG) 6000 0.1 M tri-Sodium citrate, pH 5.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Type: OTHER / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 29, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.98→73.24 Å / Num. obs: 21885 / % possible obs: 99.9 % / Redundancy: 5.6 % / Biso Wilson estimate: 84.05 Å2 / CC1/2: 0.97 / Rsym value: 0.2 / Net I/σ(I): 5.5 |
Reflection shell | Resolution: 2.98→3.16 Å / Redundancy: 5 % / Rmerge(I) obs: 1.354 / Mean I/σ(I) obs: 1.3 / Num. unique all: 3437 / CC1/2: 0.429 / Rsym value: 1.096 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2W80 Resolution: 2.98→59.7 Å / Cor.coef. Fo:Fc: 0.89 / Cor.coef. Fo:Fc free: 0.839 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 1.173 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 1.113 / SU Rfree Blow DPI: 0.383 / SU Rfree Cruickshank DPI: 0.391 Details: The target-structure restraints option (LSSR) was used while refining in BUSTER, using as fixed coordinates those of fHbp (chain A of this entry) from PDB 2YPV.
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Displacement parameters | Biso mean: 69.63 Å2
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Refine analyze | Luzzati coordinate error obs: 0.47 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.98→59.7 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.98→3.12 Å / Rfactor Rfree error: 0 / Total num. of bins used: 11
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