+Open data
-Basic information
Entry | Database: PDB / ID: 3x3g | ||||||
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Title | Fab fragment from anti TRAIL-R2 Human Agonist Antibody KMTR2 | ||||||
Components |
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Keywords | IMMUNE SYSTEM / AGONIST ANTIBODY / anti TRAIL-R2 | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta Function and homology information | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.51 Å | ||||||
Authors | Tamada, T. | ||||||
Citation | Journal: Sci Rep / Year: 2015 Title: TRAIL-R2 Superoligomerization Induced by Human Monoclonal Agonistic Antibody KMTR2 Authors: Tamada, T. / Shinmi, D. / Ikeda, M. / Yonezawa, Y. / Kataoka, S. / Kuroki, R. / Mori, E. / Motoki, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3x3g.cif.gz | 184.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3x3g.ent.gz | 147.8 KB | Display | PDB format |
PDBx/mmJSON format | 3x3g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x3/3x3g ftp://data.pdbj.org/pub/pdb/validation_reports/x3/3x3g | HTTPS FTP |
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-Related structure data
Related structure data | 3x3fSC 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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Unit cell |
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Components on special symmetry positions |
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-Components
-Antibody , 2 types, 2 molecules HL
#1: Antibody | Mass: 24899.777 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster) |
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#2: Antibody | Mass: 23350.908 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster) |
-Sugars , 1 types, 1 molecules
#3: Sugar | ChemComp-NAG / |
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-Non-polymers , 3 types, 47 molecules
#4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Sequence details | THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT ...THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEB |
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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: 4.28 Å3/Da / Density % sol: 71.26 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.6 Details: 20% PEG3350, 0.2M sodium sulfate, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 3, 2009 |
Radiation | Monochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→38.3 Å / Num. all: 27370 / Num. obs: 27370 / % possible obs: 95.4 % / Observed criterion σ(I): -3 / Redundancy: 6.3 % / Rsym value: 0.063 / Net I/σ(I): 27.6 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 3.8 / Num. unique all: 2279 / Rsym value: 0.396 / % possible all: 81.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3X3F Resolution: 2.51→38.25 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.94 / SU B: 16.846 / SU ML: 0.172 / Cross valid method: THROUGHOUT / ESU R: 0.255 / ESU R Free: 0.211 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 78.149 Å2
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Refinement step | Cycle: LAST / Resolution: 2.51→38.25 Å
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Refine LS restraints |
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