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Yorodumi- PDB-2a6i: Crystal structure analysis of the anti-arsonate germline antibody... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2a6i | ||||||
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Title | Crystal structure analysis of the anti-arsonate germline antibody 36-65 in complex with a phage display derived dodecapeptide KLASIPTHTSPL | ||||||
Components |
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Keywords | IMMUNE SYSTEM / Immunoglobulin fold / Fab-peptide complex | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta Function and homology information | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Sethi, D.K. / Agarwal, A. / Manivel, V. / Rao, K.V. / Salunke, D.M. | ||||||
Citation | Journal: Immunity / Year: 2006 Title: Differential epitope positioning within the germline antibody paratope enhances promiscuity in the primary immune response. Authors: Sethi, D.K. / Agarwal, A. / Manivel, V. / Rao, K.V. / Salunke, D.M. | ||||||
History |
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Remark 999 | SEQUENCE THE SEQUENCE IS NOT DEPOSITED IN ANY SEQUENCE DATABASE EXCEPT RESIDUES 1 TO 120 OF CHAINS ...SEQUENCE THE SEQUENCE IS NOT DEPOSITED IN ANY SEQUENCE DATABASE EXCEPT RESIDUES 1 TO 120 OF CHAINS B,H WHICH CORRESPOND TO DEPOSITED SEQUENCE OF THE HEAVY CHAIN VARIABLE REGION OF ANTI-ARSONATE ANTIBODY 36-65 |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2a6i.cif.gz | 92.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2a6i.ent.gz | 75 KB | Display | PDB format |
PDBx/mmJSON format | 2a6i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a6/2a6i ftp://data.pdbj.org/pub/pdb/validation_reports/a6/2a6i | 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: Antibody | Mass: 23707.049 Da / Num. of mol.: 1 / Fragment: Fab / Source method: isolated from a natural source / Details: Mouse monoclonal / Source: (natural) Mus musculus (house mouse) |
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#2: Antibody | Mass: 23942.768 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Mouse monoclonal / Source: (natural) Mus musculus (house mouse) |
#3: Protein/peptide | Mass: 1266.486 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: Chemically synthesized (Phage display derived peptide) |
#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: 2.47 Å3/Da / Density % sol: 50.11 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.7 Details: 16% PEG 8000, cacodylate, 0.05% azide , pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 24, 2004 / Details: mirrors |
Radiation | Monochromator: Osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. all: 15724 / Num. obs: 15724 / % possible obs: 94.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Rmerge(I) obs: 0.104 / Net I/σ(I): 5.1 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 2.84 % / Mean I/σ(I) obs: 1.7 / % possible all: 96.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.5→50 Å
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Refine LS restraints |
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