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Yorodumi- PDB-1vpo: Crystal Structure Analysis of the Anti-testosterone Fab in Comple... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1vpo | |||||||||
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Title | Crystal Structure Analysis of the Anti-testosterone Fab in Complex with Testosterone | |||||||||
Components |
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Keywords | IMMUNE SYSTEM / fab fragment / anti-steroid / testosterone complex | |||||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / TESTOSTERONE Function and homology information | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.15 Å | |||||||||
Authors | Valjakka, J.M. / Hemminki, A. / Niemi, S. / Soderlund, H. / Takkinen, K. / Rouvinen, J. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2002 Title: Crystal Structure of an in Vitro Affinity- and Specificity-matured Anti-testosterone Fab in Complex with Testosterone. IMPROVED AFFINITY RESULTS FROM SMALL STRUCTURAL CHANGES WITHIN THE VARIABLE DOMAINS Authors: Valjakka, J.M. / Hemminki, A. / Niemi, S. / Soderlund, H. / Takkinen, K. / Rouvinen, J. | |||||||||
History |
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Remark 999 | sequence an appropriate sequence database reference was not available at the time of processing. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1vpo.cif.gz | 104.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1vpo.ent.gz | 78.5 KB | Display | PDB format |
PDBx/mmJSON format | 1vpo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1vpo_validation.pdf.gz | 714.8 KB | Display | wwPDB validaton report |
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Full document | 1vpo_full_validation.pdf.gz | 729.3 KB | Display | |
Data in XML | 1vpo_validation.xml.gz | 22.6 KB | Display | |
Data in CIF | 1vpo_validation.cif.gz | 31.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vp/1vpo ftp://data.pdbj.org/pub/pdb/validation_reports/vp/1vpo | HTTPS FTP |
-Related structure data
Related structure data | 1l7tC 1i9jS 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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2 |
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Unit cell |
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-Components
#1: Antibody | Mass: 24151.910 Da / Num. of mol.: 1 / Fragment: fab77 fragment Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pKKtac / Production host: Escherichia coli (E. coli) / Strain (production host): RV308 |
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#2: Antibody | Mass: 23583.697 Da / Num. of mol.: 1 / Fragment: fab77 fragment Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pKKtac / Production host: Escherichia coli (E. coli) / Strain (production host): RV308 |
#3: Chemical | ChemComp-TES / |
#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: 2.46 Å3/Da / Density % sol: 49.92 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 Details: Peg 3350, MES, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jun 14, 1998 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→99 Å / Num. obs: 23102 / % possible obs: 97 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.057 |
Reflection shell | Resolution: 2.15→2.23 Å / % possible all: 33 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1I9J Resolution: 2.15→50 Å / σ(F): 1
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Solvent computation | Bsol: 53.4872 Å2 / ksol: 0.316428 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.15→50 Å
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Refine LS restraints |
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Xplor file |
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