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Open data
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Basic information
Entry | Database: PDB / ID: 4yhy | |||||||||
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Title | Crystal structure of 309M3-B in complex with trimethylated Lys | |||||||||
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![]() | IMMUNE SYSTEM / Antibody / Fab / Trimethylated Lys | |||||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / N-TRIMETHYLLYSINE![]() | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Hattori, T. / Dementieva, I.S. / Montano, S.P. / Koide, S. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Antigen clasping by two antigen-binding sites of an exceptionally specific antibody for histone methylation. Authors: Hattori, T. / Lai, D. / Dementieva, I.S. / Montano, S.P. / Kurosawa, K. / Zheng, Y. / Akin, L.R. / Swist-Rosowska, K.M. / Grzybowski, A.T. / Koide, A. / Krajewski, K. / Strahl, B.D. / ...Authors: Hattori, T. / Lai, D. / Dementieva, I.S. / Montano, S.P. / Kurosawa, K. / Zheng, Y. / Akin, L.R. / Swist-Rosowska, K.M. / Grzybowski, A.T. / Koide, A. / Krajewski, K. / Strahl, B.D. / Kelleher, N.L. / Ruthenburg, A.J. / Koide, S. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 187.9 KB | Display | ![]() |
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PDB format | ![]() | 146.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4yhpC ![]() 4yhzC ![]() 1mhpS ![]() 2dd8S ![]() 2r8sS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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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: 23269.580 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Antibody | Mass: 24670.701 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.76 Å3/Da / Density % sol: 55.38 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 24% PEG 3350, 10% Tacsimate (pH7.0), 10 mM EDTA, 1% MPD, 10 mM Sarcosine |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 20, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 79791 / % possible obs: 98.6 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 25.4 |
Reflection shell | Resolution: 1.9→1.93 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.587 / Mean I/σ(I) obs: 2.5 / % possible all: 84.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2R8S, 2DD8, 1MHP Resolution: 1.9→39.848 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.51 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→39.848 Å
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Refine LS restraints |
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LS refinement shell |
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