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Yorodumi- PDB-2cju: Crystal structure of the TEPC15-Vk45.1 anti-2-phenyl-5-oxazolone ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2cju | ||||||
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Title | Crystal structure of the TEPC15-Vk45.1 anti-2-phenyl-5-oxazolone NQ16- 113.8 scFv in complex with phOxGABA | ||||||
Components | (NQ16-113.8 ANTI-PHOX ANTIBODY) x 2 | ||||||
Keywords | IMMUNE SYSTEM / SCFV / ANTIBODY / IMMUNOGLOBULIN / 2-PHENYL-5-OXAZOLONE / IMMUNOGLOBULIN DOMAIN | ||||||
Function / homology | Function and homology information immunoglobulin complex / immunoglobulin mediated immune response / antigen binding Similarity search - Function | ||||||
Biological species | MUS MUSCULUS (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Scotti, C. / Gherardi, E. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2006 Title: Structural Basis of Affinity Maturation of the Tepc15/V(Kappa)45.1 Anti-2-Phenyl-5-Oxazolone Antibodies. Authors: Scotti, C. / Gherardi, E. | ||||||
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 | 2cju.cif.gz | 60.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2cju.ent.gz | 43.2 KB | Display | PDB format |
PDBx/mmJSON format | 2cju.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2cju_validation.pdf.gz | 699.9 KB | Display | wwPDB validaton report |
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Full document | 2cju_full_validation.pdf.gz | 715.7 KB | Display | |
Data in XML | 2cju_validation.xml.gz | 13.9 KB | Display | |
Data in CIF | 2cju_validation.cif.gz | 17.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cj/2cju ftp://data.pdbj.org/pub/pdb/validation_reports/cj/2cju | HTTPS FTP |
-Related structure data
Related structure data | 2uudC 1flrS C: citing same article (ref.) 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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Components on special symmetry positions |
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-Components
#1: Antibody | Mass: 13390.922 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MUS MUSCULUS (house mouse) / Strain: BALB/C / Description: NQ16/113.8 ANTI-2-PHENYL-5-OXAZOLONE HYBRIDOMA / Cell: HYBRIDOMA / Plasmid: PPIC9KE / Production host: PICHIA PASTORIS (fungus) / Strain (production host): GS115 / References: UniProt: P01789*PLUS |
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#2: Antibody | Mass: 12423.988 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MUS MUSCULUS (house mouse) / Strain: BALB/C / Description: NQ16/113.8 ANTI-2-PHENYL-5-OXAZOLONE HYBRIDOMA / Cell: HYBRIDOMA / Plasmid: PPIC9KE / Production host: PICHIA PASTORIS (fungus) / Strain (production host): GS115 |
#3: Chemical | ChemComp-PHX / |
#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: 2.4 Å3/Da / Density % sol: 49 % / Description: NONE |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8.4 Details: 0.1 M TRIS-HCL, PH 8.4, 0.2 M AMMONIUM SULPHATE, 37% PEG 8K, 6% SUCROSE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.933 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Sep 29, 2002 / Details: MIRRORS |
Radiation | Monochromator: DIAMOND (111) GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→30 Å / Num. obs: 17246 / % possible obs: 97.4 % / Redundancy: 3.1 % / Biso Wilson estimate: 20.9 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 10.8 |
Reflection shell | Resolution: 2.5→2.7 Å / Redundancy: 1.2 % / Rmerge(I) obs: 0.34 / % possible all: 89.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1FLR Resolution: 2.5→30 Å / Rfactor Rfree error: 0.014 / Data cutoff high absF: 1470440 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MLF
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 28.7 Å2 / ksol: 0.39 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.59 Å / Rfactor Rfree error: 0.069 / Total num. of bins used: 10
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Xplor file |
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