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- PDB-5o1r: human Fab 5H2 bound to NHBA-C3 from Neisseria meningitidis serogroup B -
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Open data
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Basic information
Entry | Database: PDB / ID: 5o1r | ||||||
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Title | human Fab 5H2 bound to NHBA-C3 from Neisseria meningitidis serogroup B | ||||||
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![]() | IMMUNE SYSTEM | ||||||
Function / homology | ![]() immunoglobulin complex, circulating / immunoglobulin receptor binding / complement activation, classical pathway / antigen binding / cell outer membrane / heparin binding / antibacterial humoral response / blood microparticle / cell adhesion / immune response ...immunoglobulin complex, circulating / immunoglobulin receptor binding / complement activation, classical pathway / antigen binding / cell outer membrane / heparin binding / antibacterial humoral response / blood microparticle / cell adhesion / immune response / DNA binding / extracellular space / extracellular exosome / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Malito, E. / Maritan, M. | ||||||
![]() | ![]() Title: Structures of NHBA elucidate a broadly conserved epitope identified by a vaccine induced antibody. Authors: Maritan, M. / Veggi, D. / Cozzi, R. / Dello Iacono, L. / Bartolini, E. / Lo Surdo, P. / Maruggi, G. / Spraggon, G. / Bottomley, M.J. / Malito, E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 428.5 KB | Display | ![]() |
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PDB format | ![]() | 353.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5nyxSC ![]() 6cujC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 13706.022 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Antibody | Mass: 27962.980 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: the sequence provided includes the tag which was cleaved prior to crystallization Source: (gene. exp.) ![]() ![]() #3: Antibody | Mass: 23094.561 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #4: Chemical | ChemComp-EDO / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.9 Å3/Da / Density % sol: 57.52 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 0.1 M TRIS pH 8.0 and 1.6 M lithium sulphate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 3, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.86→91.05 Å / Num. obs: 36688 / % possible obs: 100 % / Redundancy: 19.4 % / Biso Wilson estimate: 88.02 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.189 / Rpim(I) all: 0.044 / Rrim(I) all: 0.194 / Net I/σ(I): 18.4 |
Reflection shell | Resolution: 2.86→2.93 Å / Mean I/σ(I) obs: 1 / Num. unique obs: 2628 / CC1/2: 0.557 / Rpim(I) all: 0.875 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5NYX Resolution: 2.86→78.74 Å / Cor.coef. Fo:Fc: 0.9465 / Cor.coef. Fo:Fc free: 0.9196 / SU R Cruickshank DPI: 0.826 / Cross valid method: FREE R-VALUE / σ(F): 0 / SU R Blow DPI: 0.926 / SU Rfree Blow DPI: 0.301 / SU Rfree Cruickshank DPI: 0.303
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Displacement parameters | Biso mean: 84.55 Å2
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Refine analyze | Luzzati coordinate error obs: 0.447 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.86→78.74 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.86→2.94 Å / Total num. of bins used: 18
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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