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Yorodumi- PDB-5xcr: Crystal structure of P20.1 Fv-clasp fragment with its antigen peptide -
+Open data
-Basic information
Entry | Database: PDB / ID: 5xcr | ||||||
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Title | Crystal structure of P20.1 Fv-clasp fragment with its antigen peptide | ||||||
Components |
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Keywords | IMMUNE SYSTEM / antibody fragment / Fv-clasp | ||||||
Function / homology | p53, subunit A / p53-like tetramerisation domain / Few Secondary Structures / Irregular / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta Function and homology information | ||||||
Biological species | Mus musculus (house mouse) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Arimori, T. / Takagi, J. | ||||||
Citation | Journal: Structure / Year: 2017 Title: Fv-clasp: An Artificially Designed Small Antibody Fragment with Improved Production Compatibility, Stability, and Crystallizability Authors: Arimori, T. / Kitago, Y. / Umitsu, M. / Fujii, Y. / Asaki, R. / Tamura-Kawakami, K. / Takagi, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5xcr.cif.gz | 282.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5xcr.ent.gz | 228.7 KB | Display | PDB format |
PDBx/mmJSON format | 5xcr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5xcr_validation.pdf.gz | 453.1 KB | Display | wwPDB validaton report |
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Full document | 5xcr_full_validation.pdf.gz | 454 KB | Display | |
Data in XML | 5xcr_validation.xml.gz | 29.7 KB | Display | |
Data in CIF | 5xcr_validation.cif.gz | 44.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xc/5xcr ftp://data.pdbj.org/pub/pdb/validation_reports/xc/5xcr | HTTPS FTP |
-Related structure data
Related structure data | 5xcqSC 5xcsC 5xctC 5xcuC 5xcvC 5xcxC S: Starting model for refinement C: citing same article (ref.) |
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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: 19116.740 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: ? Source: (gene. exp.) Mus musculus (house mouse), (gene. exp.) Homo sapiens (human) Production host: Escherichia coli (E. coli) #2: Antibody | Mass: 18148.316 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse), (gene. exp.) Homo sapiens (human) Production host: Escherichia coli (E. coli) #3: Protein/peptide | Mass: 873.976 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 50.69 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / Details: 0.1M Citrate (pH 5.5), 20%(w/v) PEG3000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Oct 4, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→46.66 Å / Num. obs: 75053 / % possible obs: 99.9 % / Redundancy: 7.6 % / Rsym value: 0.09 / Net I/σ(I): 16.69 |
Reflection shell | Resolution: 1.75→1.86 Å / Redundancy: 7.5 % / Mean I/σ(I) obs: 3.22 / Rsym value: 0.71 / % possible all: 99.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5XCQ Resolution: 1.75→46.66 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.944 / SU B: 4.43 / SU ML: 0.072 / Cross valid method: THROUGHOUT / ESU R: 0.106 / ESU R Free: 0.103 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.234 Å2
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Refinement step | Cycle: 1 / Resolution: 1.75→46.66 Å
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Refine LS restraints |
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