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Yorodumi- PDB-1e4x: crossreactive binding of a circularized peptide to an anti-TGFalp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1e4x | ||||||
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Title | crossreactive binding of a circularized peptide to an anti-TGFalpha antibody Fab-fragment | ||||||
Components |
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Keywords | IMMUNE SYSTEM / COMPLEX (ANTIBODY-ANTIGEN) / CROSS-REACTIVITY / PROTEIN-PEPTIDE RECOGNITION | ||||||
Function / homology | Function and homology information | ||||||
Biological species | MUS MUSCULUS (house mouse) SYNTHETIC CONSTRUCT (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Hahn, M. / Winkler, D. / Misselwitz, R. / Wessner, H. / Welfle, K. / Zahn, G. / Schneider-Mergener, J. / Hoehne, W. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2001 Title: Cross-Reactive Binding of Cyclic Peptides to an Anti-Tgf Alpha Antibody Fab Fragment: An X-Ray Structural and Thermodynamic Analysis Authors: Hahn, M. / Winkler, D. / Welfle, K. / Misselwitz, R. / Welfle, H. / Wessner, H. / Zahn, G. / Scholz, C. / Seifert, M. / Harkins, R. / Schneider-Mergener, J. / Hoehne, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1e4x.cif.gz | 184.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1e4x.ent.gz | 146.6 KB | Display | PDB format |
PDBx/mmJSON format | 1e4x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e4/1e4x ftp://data.pdbj.org/pub/pdb/validation_reports/e4/1e4x | HTTPS FTP |
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-Related 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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.23405, -0.18859, -0.95376), Vector: |
-Components
#1: Antibody | Mass: 23351.205 Da / Num. of mol.: 1 / Fragment: IG KAPPA HEAVY CHAIN / Source method: isolated from a natural source / Details: MURINE FAB-FRAGMENT / Source: (natural) MUS MUSCULUS (house mouse) / Cell line: MOUSE HYBRIDOMA / Organ: SPLEEN | ||||||
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#2: Antibody | Mass: 23377.242 Da / Num. of mol.: 1 / Fragment: IG KAPPA HEAVY CHAIN / Source method: isolated from a natural source / Details: MURINE FAB-FRAGMENT / Source: (natural) MUS MUSCULUS (house mouse) / Cell line: MOUSE HYBRIDOMA / Organ: SPLEEN | ||||||
#3: Antibody | Mass: 23577.947 Da / Num. of mol.: 2 / Fragment: IG KAPPA LIGHT CHAIN / Source method: isolated from a natural source / Details: MURINE FAB-FRAGMENT / Source: (natural) MUS MUSCULUS (house mouse) / Cell line: MOUSE HYBRIDOMA / Organ: SPLEEN / Strain: BALB/C / References: UniProt: P01837*PLUS #4: Protein/peptide | Mass: 817.866 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others) #5: Water | ChemComp-HOH / | Compound details | CHAIN P IS A EPITOPE PEPTIDE WITH THE SEQUENCE VAL-VAL-SER-HIS-PHE-ASN-ASP, DERIVED FROM THE N- ...CHAIN P IS A EPITOPE PEPTIDE WITH THE SEQUENCE VAL-VAL-SER-HIS-PHE-ASN-ASP, DERIVED FROM THE N-TERMINUS OF TGFALPHA. CHAIN L, M: THE C-TERMINAL REGION IS THE CONSTANT REGION OF THE IG KAPPA LIGHT CHAIN. THE N-TERMINAL REGION IS THE VARIABLE REGION OF THE IG KAPPA LIGHT CHAIN. THE VARIABLE REGION IS AUTOANTIBO | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 40.7 % | ||||||||||||||||||||
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Crystal grow | pH: 8.5 Details: PROTEIN IN TRIS-HCL, 8.5, 6-10 MG/ML PRECIPITANT: 12% PEG 8000, 20 MM NA-ACETATE, pH 8.50 | ||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.3 |
Detector | Type: XRAY RESEARCH / Detector: CCD / Date: Jun 17, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.3 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→20 Å / Num. obs: 68086 / % possible obs: 92.9 % / Redundancy: 5.2 % / Biso Wilson estimate: 22.7 Å2 / Rmerge(I) obs: 0.038 / Net I/σ(I): 29.7 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.257 / Mean I/σ(I) obs: 2.4 / % possible all: 82.8 |
Reflection | *PLUS Lowest resolution: 20 Å |
Reflection shell | *PLUS % possible obs: 82.8 % / Mean I/σ(I) obs: 2.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: TAB2 Resolution: 1.9→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 36 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→20 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 20 Å / Rfactor obs: 0.245 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |