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Yorodumi- PDB-1f90: FAB FRAGMENT OF MONOCLONAL ANTIBODY (LNKB-2) AGAINST HUMAN INTERL... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1f90 | ||||||
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Title | FAB FRAGMENT OF MONOCLONAL ANTIBODY (LNKB-2) AGAINST HUMAN INTERLEUKIN-2 IN COMPLEX WITH ANTIGENIC PEPTIDE | ||||||
Components |
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Keywords | IMMUNE SYSTEM / monoclonal antibody / antigen-binding fragment / interleukin-2 / antigenic peptide | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta Function and homology information | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.6 Å | ||||||
Authors | Afonin, P.V. / Fokin, A.V. / Tsigannik, I.N. / Mikhailova, I.Y. / Onoprienko, L.V. / Mikhaleva, I.I. / Ivanov, V.T. / Mareeva, T.Y. / Nesmeyanov, V.A. / Li, N. ...Afonin, P.V. / Fokin, A.V. / Tsigannik, I.N. / Mikhailova, I.Y. / Onoprienko, L.V. / Mikhaleva, I.I. / Ivanov, V.T. / Mareeva, T.Y. / Nesmeyanov, V.A. / Li, N. / Duax, W.L. / Pletnev, V.Z. | ||||||
Citation | Journal: Protein Sci. / Year: 2001 Title: Crystal structure of an anti-interleukin-2 monoclonal antibody Fab complexed with an antigenic nonapeptide. Authors: Afonin, P.V. / Fokin, A.V. / Tsygannik, I.N. / Mikhailova, I.Y. / Onoprienko, L.V. / Mikhaleva, I.I. / Ivanov, V.T. / Mareeva, T.Y. / Nesmeyanov, V.A. / Li, N. / Pangborn, W.A. / Duax, W.L. / Pletnev, V.Z. #1: Journal: BIOORG.KHIM. / Year: 2000 Title: THREE-DIMENSIONAL STRUCTURE OF ANTIGEN BINDING FRAGMENT OF MONOCLONAL ANTIBODY AGAINST HUMAN INTERLEUKIN-2 IN TWO CRYSTAL FORMS AT 2.2 AND 2.9 A RESOLUTION. Authors: Fokin, A.V. / Afonin, P.V. / Mikhailova, I.Y. / Tsygannik, I.N. / Mareeva, T.Y. / Nesmeyanov, V.A. / Pangborn, W. / Lee, N. / Duax, W. / Sijak, E. / Pletnev, V.Z. | ||||||
History |
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Remark 999 | SEQUENCE The sequence of the protein has not been deposited in any sequence database. It was ...SEQUENCE The sequence of the protein has not been deposited in any sequence database. It was published in the Bioorganicheskaya Khimiya (Rus) (1995), V21, N6, p430-435. "Cloning cDNA Encoding Fv-Fragments of the Light and Heavy Chains of the Monoclonal Antibody" by A.I.Paskhin, T.N. Golovina, V.A. Nesmeyanov, V.G. Korobko. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1f90.cif.gz | 96.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1f90.ent.gz | 78.1 KB | Display | PDB format |
PDBx/mmJSON format | 1f90.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f9/1f90 ftp://data.pdbj.org/pub/pdb/validation_reports/f9/1f90 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Antibody | Mass: 24203.908 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell line: HYBRIDOMA |
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#2: Antibody | Mass: 23853.600 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell line: HYBRIDOMA |
#3: Protein/peptide | Mass: 1055.244 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: The Peptide was Chemically Synthetized in Solution |
#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: 2.39 Å3/Da / Density % sol: 48.59 % | |||||||||||||||||||||||||
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: PEG-4000, 2-propanol, Na-citrate , pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 300.0K | |||||||||||||||||||||||||
Crystal grow | *PLUS | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 300 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Feb 5, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→99 Å / Num. all: 13733 / Num. obs: 11984 / % possible obs: 83.4 % / Observed criterion σ(F): 2 / Redundancy: 4.3 % / Rmerge(I) obs: 0.148 / Net I/σ(I): 6.9 |
Reflection shell | Resolution: 2.6→2.73 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.5825 / Num. unique all: 1850 / % possible all: 97.15 |
Reflection | *PLUS Num. obs: 9377 / % possible obs: 99.7 % / Num. measured all: 19271 / Rmerge(I) obs: 0.112 |
-Processing
Software |
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Refinement | Resolution: 2.6→99 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber Details: Cross-validated maximum likelihood simulated annealing refinement (CNS package)
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Refinement step | Cycle: LAST / Resolution: 2.6→99 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Version: 0.9 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.6 Å / Lowest resolution: 99 Å / σ(F): 2 / % reflection Rfree: 5 % / Rfactor obs: 0.18 / Rfactor Rfree: 0.263 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: c_angle_deg / Dev ideal: 1.4 |