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Yorodumi- PDB-2ypv: Crystal structure of the Meningococcal vaccine antigen factor H b... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ypv | ||||||
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Title | Crystal structure of the Meningococcal vaccine antigen factor H binding protein in complex with a bactericidal antibody | ||||||
Components |
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Keywords | IMMUNE SYSTEM / VACCINE / MONOCLONAL ANTIBODY / MAB / EPITOPE MAPPING | ||||||
Function / homology | Function and homology information | ||||||
Biological species | NEISSERIA MENINGITIDIS MC58 (bacteria) MUS MUSCULUS (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Malito, E. / Veggi, D. / Bottomley, M.J. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2013 Title: Defining a Protective Epitope on Factor H Binding Protein, a Key Meningococcal Virulence Factor and Vaccine Antigen. Authors: Malito, E. / Faleri, A. / Lo Surdo, P. / Veggi, D. / Maruggi, G. / Grassi, E. / Cartocci, E. / Bertoldi, I. / Genovese, A. / Santini, L. / Romagnoli, G. / Borgogni, E. / Brier, S. / Lo ...Authors: Malito, E. / Faleri, A. / Lo Surdo, P. / Veggi, D. / Maruggi, G. / Grassi, E. / Cartocci, E. / Bertoldi, I. / Genovese, A. / Santini, L. / Romagnoli, G. / Borgogni, E. / Brier, S. / Lo Passo, C. / Domina, M. / Castellino, F. / Felici, F. / Van Der Veen, S. / Johnson, S. / Lea, S.M. / Tang, C.M. / Pizza, M. / Savino, S. / Norais, N. / Rappuoli, R. / Bottomley, M.J. / Masignani, V. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AC" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AC" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ypv.cif.gz | 151.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ypv.ent.gz | 116.7 KB | Display | PDB format |
PDBx/mmJSON format | 2ypv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yp/2ypv ftp://data.pdbj.org/pub/pdb/validation_reports/yp/2ypv | HTTPS FTP |
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-Related 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 MC58 (bacteria) / Variant: 1.1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6QCC2, UniProt: Q9JXV4*PLUS | ||||
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#2: Antibody | Mass: 23395.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) MUS MUSCULUS (house mouse) | ||||
#3: Antibody | Mass: 23844.354 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) MUS MUSCULUS (house mouse) | ||||
#4: Chemical | ChemComp-EDO / #5: Water | ChemComp-HOH / | Sequence details | THE MAB 12C1 WAS FULLY SEQUENCED ISOLATING RNA FROM MURINE HYBRIDOMA CELLS, FROM WHICH CDNA WAS ...THE MAB 12C1 WAS FULLY SEQUENCED ISOLATING RNA FROM MURINE HYBRIDOMA CELLS, FROM WHICH CDNA WAS PREPARED USING STANDARD METHODS. THE MAB HEAVY AND LIGHT CHAINS WERE AMPLIFIED FROM THE CDNA BY PCR USING A SET OF DEGENERATE | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.81 % / Description: NONE |
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Crystal grow | pH: 8.5 / Details: 20% PEG 3350, 0.2M AMMONIUM SULFATE, pH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jan 30, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→39.53 Å / Num. obs: 69157 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 6.1 % / Biso Wilson estimate: 22.54 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 12.62 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.83 / Mean I/σ(I) obs: 2.02 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRIES 2W80 1KB5 3LIZ Resolution: 1.8→39.531 Å / SU ML: 0.2 / σ(F): 1.33 / Phase error: 22.11 / Stereochemistry target values: ML Details: DISORDERED REGIONS IN CHAIN A INCLUDE RESIDUES V8-A14 E83- Q87 AND Q115-K122. DISORDERED REGION IN CHAIN H INCLUDE RESIDUES G135-T137.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.4 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→39.531 Å
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Refine LS restraints |
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LS refinement shell |
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