[English] 日本語
Yorodumi- PDB-2xzc: Crystal Structure of phosphonate-modified recombinant A.17 antibo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2xzc | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal Structure of phosphonate-modified recombinant A.17 antibody FAB fragment | |||||||||
Components |
| |||||||||
Keywords | IMMUNE SYSTEM | |||||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Chem-XOP Function and homology information | |||||||||
Biological species | HOMO SAPIENS (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.36 Å | |||||||||
Authors | Carletti, E. / Nachon, F. / Nicolet, Y. / Masson, P. / Kurkova, I. / Smirnov, I. / Friboulet, A. / Tramontano, A. / Gabibov, A. | |||||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2011 Title: Reactibodies Generated by Kinetic Selection Couple Chemical Reactivity with Favorable Protein Dynamics. Authors: Smirnov, I. / Carletti, E. / Kurkova, I. / Nachon, F. / Nicolet, Y. / Mitkevich, V.A. / Debat, H. / Avalle, B. / Belogurov, A.A. / Kuznetsov, N. / Reshetnyak, A. / Masson, P. / Tonevitsky, A. ...Authors: Smirnov, I. / Carletti, E. / Kurkova, I. / Nachon, F. / Nicolet, Y. / Mitkevich, V.A. / Debat, H. / Avalle, B. / Belogurov, A.A. / Kuznetsov, N. / Reshetnyak, A. / Masson, P. / Tonevitsky, A.G. / Ponomarenko, N. / Makarov, A.A. / Friboulet, A. / Tramontano, A. / Gabibov, A. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2xzc.cif.gz | 113.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2xzc.ent.gz | 90.6 KB | Display | PDB format |
PDBx/mmJSON format | 2xzc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xz/2xzc ftp://data.pdbj.org/pub/pdb/validation_reports/xz/2xzc | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Antibody | Mass: 23322.961 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): CHO / Production host: CRICETULUS GRISEUS (Chinese hamster) |
---|---|
#2: Antibody | Mass: 23140.525 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): CHO / Production host: CRICETULUS GRISEUS (Chinese hamster) |
#3: Chemical | ChemComp-CL / |
#4: Chemical | ChemComp-XOP / |
#5: Water | ChemComp-HOH / |
Nonpolymer details | 8-METHYL-8-AZABICYCLO[3.2.1]OCTAN-3-YL PHENYLPHOSPHONATE (XOP): THE LIGAND XOP IS COVALENTLY BOND ...8-METHYL-8-AZABICYCLO |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.9 % / Description: NONE |
---|---|
Crystal grow | pH: 6.5 / Details: 0.1M ADA BUFFER PH 6.5, 0.1M MGCL2, 20% PEG6000 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.979 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 19, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.36→50 Å / Num. obs: 92464 / % possible obs: 98.5 % / Observed criterion σ(I): 3 / Redundancy: 3.6 % / Biso Wilson estimate: 61.34 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 27.8 |
Reflection shell | Resolution: 1.36→1.4 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 4.7 / % possible all: 99.9 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: OTHER Starting model: NONE Resolution: 1.36→38.32 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.961 / SU B: 0.898 / SU ML: 0.037 / Cross valid method: THROUGHOUT / ESU R: 0.053 / ESU R Free: 0.057 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.962 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.36→38.32 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|