[English] 日本語
Yorodumi- PDB-2uud: Crystal structure of the TEPC15-Vk45.1 anti-2-phenyl-5-oxazolone ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2uud | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of the TEPC15-Vk45.1 anti-2-phenyl-5-oxazolone NQ10- 1.12 scFv in complex with the hapten | |||||||||
Components | (NQ10-1.12 ANTI-PHOX ANTIBODY) x 3 | |||||||||
Keywords | IMMUNE SYSTEM / SCFV / ANTIBODY / IMMUNOGLOBULIN / 2-PHENYL-5-OXAZOLONE / IMMUNOGLOBULIN DOMAIN | |||||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Chem-PHX Function and homology information | |||||||||
Biological species | MUS MUSCULUS (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | |||||||||
Authors | Scotti, C. / Gherardi, E. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 2006 Title: Structural Basis of Affinity Maturation of the Tepc15-Vkappa45.1 Anti-2-Phenyl-5-Oxazolone Antibodies Authors: Scotti, C. / Gherardi, E. | |||||||||
History |
| |||||||||
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 |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2uud.cif.gz | 107.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2uud.ent.gz | 83 KB | Display | PDB format |
PDBx/mmJSON format | 2uud.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2uud_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2uud_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 2uud_validation.xml.gz | 27.3 KB | Display | |
Data in CIF | 2uud_validation.cif.gz | 35.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uu/2uud ftp://data.pdbj.org/pub/pdb/validation_reports/uu/2uud | HTTPS FTP |
-Related structure data
Related structure data | 2cjuC 1flrS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||||||
2 |
| ||||||||||||||||
Unit cell |
| ||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS oper:
|
-Components
#1: Antibody | Mass: 13410.949 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MUS MUSCULUS (house mouse) / Strain: BALB/C / Description: NQ10/1.12 ANTI-2-PHENYL-5-OXAZOLONE HYBRIDOMA / Cell: HYBRIDOMA / Plasmid: PPIC9KE / Production host: PICHIA PASTORIS (fungus) / Strain (production host): GS115 #2: Antibody | Mass: 12423.988 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MUS MUSCULUS (house mouse) / Strain: BALB/C / Description: NQ10/1.12 ANTI-2-PHENYL-5-OXAZOLONE HYBRIDOMA / Cell: HYBRIDOMA / Plasmid: PPIC9KE / Production host: PICHIA PASTORIS (fungus) / Strain (production host): GS115 #3: Antibody | Mass: 1283.182 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MUS MUSCULUS (house mouse) / Strain: BALB/C / Description: NQ10/1.12 ANTI-2-PHENYL-5-OXAZOLONE HYBRIDOMA / Cell: HYBRIDOMA / Plasmid: PPIC9KE / Production host: PICHIA PASTORIS (fungus) / Strain (production host): GS115 #4: Chemical | #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.32 % |
---|---|
Crystal grow | pH: 7.6 Details: 0.1 M TRIS-HCL, PH 7.6, 0.2 M AMMONIUM SULPHATE, 30% PEG 4K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 1 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Feb 13, 2002 / Details: MIRRORS |
Radiation | Monochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→65.64 Å / Num. obs: 11988 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Biso Wilson estimate: 75.3 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 9.6 |
Reflection shell | Resolution: 2.9→3 Å / Rmerge(I) obs: 0.22 / % possible all: 99.1 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1FLR Resolution: 2.9→19.9 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 809326.5 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Details: FOR REFINEMENT-REBUILDING, THE PROGRAM LAFIRE HAS BEEN USED, STARTING FROM THE 2CJV STRUCTURE
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 45.3383 Å2 / ksol: 0.336356 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→19.9 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.9→2.99 Å / Rfactor Rfree error: 0.054 / Total num. of bins used: 11
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
|