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Yorodumi- PDB-2brr: Complex of the neisserial PorA P1.4 epitope peptide and two Fab- ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2brr | ||||||
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Title | Complex of the neisserial PorA P1.4 epitope peptide and two Fab- fragments (antibody MN20B9.34) | ||||||
Components |
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Keywords | IMMUNE SYSTEM / FAB FRAGMENT / ANTI-PORA ANTIBODY / P1.4 ANTIBODY / ANTIGEN / PORIN / TRANSMEMBRANE / ANTIBODY-ANTIGEN COMPLEX | ||||||
Function / homology | Function and homology information porin activity / monoatomic ion transmembrane transport / cell outer membrane Similarity search - Function | ||||||
Biological species | MUS MUSCULUS (house mouse) NEISSERIA MENINGITIDIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Oomen, C.J. / Hoogerhout, P. / Kuipers, B. / Vidarsson, G. / Van Alphen, L. / Gros, P. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2005 Title: Crystal Structure of an Anti-Meningococcal Subtype P1.4 Pora Antibody Provides Basis for Peptide- Vaccine Design. Authors: Oomen, C.J. / Hoogerhout, P. / Kuipers, B. / Vidarsson, G. / Van Alphen, L. / Gros, P. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2brr.cif.gz | 184.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2brr.ent.gz | 146.7 KB | Display | PDB format |
PDBx/mmJSON format | 2brr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/br/2brr ftp://data.pdbj.org/pub/pdb/validation_reports/br/2brr | HTTPS FTP |
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-Related structure data
Related structure data | 1ce1S 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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Details | THE PENTAMERIC ASSEMBLY DESCRIBED HERE IS COMPOSED OF TWO HEAVY/LIGHT CHAIN DIMERS, BOTH BOUND TO THE SINGLE CHAIN P.CHAINS H AND L ARE MARGINALLY MORE TIGHTLY BOUND TO THE PEPTIDE THAN CHAINS X AND Y |
-Components
-Protein/peptide , 1 types, 1 molecules P
#3: Protein/peptide | Mass: 1244.445 Da / Num. of mol.: 1 Fragment: EXTRACELLULAR LOOP 4 OF PORA SUBTYPE P1.4, RESIDUES 16-26 Source method: obtained synthetically / Details: N-TERMINUS ACETYLATED, C-TERMINUS AMIDATED / Source: (synth.) NEISSERIA MENINGITIDIS (bacteria) / References: UniProt: Q51183 |
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-Antibody , 2 types, 4 molecules HYLX
#1: Antibody | Mass: 24353.113 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MUS MUSCULUS (house mouse) / Cell line: MN20B9.34 MURINE HYBRIDOMA / Production host: MUS MUSCULUS (house mouse) #2: Antibody | Mass: 23427.684 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MUS MUSCULUS (house mouse) / Cell line: MN20B9.34 MURINE HYBRIDOMA / Production host: MUS MUSCULUS (house mouse) |
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-Non-polymers , 3 types, 290 molecules
#4: Chemical | #5: Chemical | ChemComp-ACY / | #6: Water | ChemComp-HOH / | |
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-Details
Sequence details | THE SEQUENCE OF CHAIN P IS GIVEN BY GENBANK ENTRY CAA78633 |
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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: 2.2 Å3/Da / Density % sol: 43 % |
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Crystal grow | pH: 4 Details: 0.2 M AMMONIUM SULPHATE, 0.1 M SODIUM ACETATE/ACETIC ACID (PH 4.0) AND 25% W/V PEG 3000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.9315 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: May 10, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9315 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→40 Å / Num. obs: 60806 / % possible obs: 96 % / Observed criterion σ(I): 1 / Redundancy: 3.5 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 14.3 |
Reflection shell | Resolution: 1.95→2.02 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 3.1 / % possible all: 92.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1CE1 Resolution: 1.95→30 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.93 / SU B: 8.458 / SU ML: 0.121 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.2 / ESU R Free: 0.17 / 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: 22.19 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→30 Å
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Refine LS restraints |
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