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- PDB-1qkz: Fab fragment (MN14C11.6) in complex with a peptide antigen derive... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1qkz | ||||||
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Title | Fab fragment (MN14C11.6) in complex with a peptide antigen derived from Neisseria meningitidis P1.7 serosubtype antigen and domain II from Streptococcal protein G | ||||||
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![]() | IMMUNE SYSTEM / FAB / PORA / NEISSERIA MENINGITIDIS / PORIN | ||||||
Function / homology | ![]() IgG binding / porin activity / pore complex / monoatomic ion transmembrane transport / cell outer membrane / extracellular region Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Derrick, J.P. / Feavers, I. / Maiden, M.C.J. | ||||||
![]() | ![]() Title: Crystal Structure of an Fab Fragment in Complex with a Meningococcal Serosubtype Antigen and a Protein G Domain Authors: Derrick, J.P. / Feavers, I.M. / Maiden, M.C.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 120.7 KB | Display | ![]() |
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PDB format | ![]() | 91.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 390.5 KB | Display | ![]() |
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Full document | ![]() | 402.2 KB | Display | |
Data in XML | ![]() | 12.3 KB | Display | |
Data in CIF | ![]() | 21.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1igcS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 7012.762 Da / Num. of mol.: 1 / Fragment: DOMAIN II / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Antibody | Mass: 23755.592 Da / Num. of mol.: 1 / Fragment: FAB / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#3: Antibody | Mass: 23954.559 Da / Num. of mol.: 1 / Fragment: FAB / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#4: Protein/peptide | Mass: 888.946 Da / Num. of mol.: 1 / Fragment: RESIDUES 4-13 / Source method: obtained synthetically / Source: (synth.) ![]() |
#5: Water | ChemComp-HOH / |
Sequence details | THE FAB ANTIBODY STUDIED HERE IS RELATED IN SEQUENCE TO THE SEQUENCES: CHAIN H TO SWS AAD40243 78 ...THE FAB ANTIBODY STUDIED HERE IS RELATED IN SEQUENCE TO THE SEQUENCES: CHAIN H TO SWS AAD40243 78 PERCENT IDENTITY GAMMA1 HEAVY CHAIN OF MAB7 MUS MUSCULUS CHAIN L TO SWS AAD40242 74 PERCENT IDENTITY KAPPA LIGHT CHAIN OF MAB7 MUS MUSCULUS THE RESIDUE NUMBERING SCHEME USED HERE IS THE KABAT NUMBERING |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.76 Å3/Da / Density % sol: 43.6 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 5 / Details: pH 5.00 | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 293 K / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→30 Å / Num. obs: 34633 / % possible obs: 98.9 % / Observed criterion σ(I): 2 / Redundancy: 5.2 % / Biso Wilson estimate: 13.7 Å2 / Rsym value: 0.037 / Net I/σ(I): 17.2 |
Reflection shell | Resolution: 1.95→2.04 Å / Rsym value: 0.125 / % possible all: 96 |
Reflection | *PLUS Num. measured all: 180259 / Rmerge(I) obs: 0.037 |
Reflection shell | *PLUS % possible obs: 96 % / Rmerge(I) obs: 0.125 |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1IGC Resolution: 1.95→10 Å / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.21
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Refinement step | Cycle: LAST / Resolution: 1.95→10 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Num. reflection obs: 32841 / Num. reflection Rfree: 1745 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |