+Open data
-Basic information
Entry | Database: PDB / ID: 4yhy | |||||||||
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Title | Crystal structure of 309M3-B in complex with trimethylated Lys | |||||||||
Components |
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Keywords | IMMUNE SYSTEM / Antibody / Fab / Trimethylated Lys | |||||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / N-TRIMETHYLLYSINE Function and homology information | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | |||||||||
Authors | Hattori, T. / Dementieva, I.S. / Montano, S.P. / Koide, S. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2016 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4yhy.cif.gz | 187.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4yhy.ent.gz | 146.7 KB | Display | PDB format |
PDBx/mmJSON format | 4yhy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4yhy_validation.pdf.gz | 457.3 KB | Display | wwPDB validaton report |
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Full document | 4yhy_full_validation.pdf.gz | 458.8 KB | Display | |
Data in XML | 4yhy_validation.xml.gz | 37.2 KB | Display | |
Data in CIF | 4yhy_validation.cif.gz | 54.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yh/4yhy ftp://data.pdbj.org/pub/pdb/validation_reports/yh/4yhy | HTTPS FTP |
-Related structure data
Related structure data | 4yhpC 4yhzC 1mhpS 2dd8S 2r8sS C: citing same article (ref.) S: Starting model for refinement |
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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: 23269.580 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): ATCC 55244 #2: Antibody | Mass: 24670.701 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): ATCC 55244 #3: Chemical | #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: 2.76 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: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.978 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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