+Open data
-Basic information
Entry | Database: PDB / ID: 6ldx | ||||||
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Title | Structure antibody E6 in complex with methylated peptide | ||||||
Components |
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Keywords | IMMUNE SYSTEM / methylation / antibody / phage display / biomolecular recognition | ||||||
Function / homology | Function and homology information mitogen-activated protein kinase kinase kinase / MAP kinase kinase kinase activity / cellular response to mechanical stimulus / protein kinase activity / intracellular signal transduction / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / protein kinase binding / nucleoplasm ...mitogen-activated protein kinase kinase kinase / MAP kinase kinase kinase activity / cellular response to mechanical stimulus / protein kinase activity / intracellular signal transduction / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / protein kinase binding / nucleoplasm / ATP binding / metal ion binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Oryctolagus cuniculus (rabbit) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Caaveiro, J.M.M. / Tsumoto, K. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2020 Title: Structural basis for antigen recognition by methylated lysine-specific antibodies. Authors: Ishii, M. / Nakakido, M. / Caaveiro, J.M.M. / Kuroda, D. / Okumura, C.J. / Maruyama, T. / Entzminger, K. / Tsumoto, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ldx.cif.gz | 182.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ldx.ent.gz | 141.6 KB | Display | PDB format |
PDBx/mmJSON format | 6ldx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ld/6ldx ftp://data.pdbj.org/pub/pdb/validation_reports/ld/6ldx | HTTPS FTP |
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-Related structure data
Related structure data | 6ldvSC 6ldwC 6ldyC 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
#1: Antibody | Mass: 25795.686 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Cell (production host): 293 / Production host: Homo sapiens (human) |
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#2: Antibody | Mass: 25361.797 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Cell (production host): 293 / Production host: Homo sapiens (human) |
#3: Protein/peptide | Mass: 1598.839 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9Y2U5*PLUS |
#4: Chemical | ChemComp-CL / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.96 Å3/Da / Density % sol: 37.38 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: 0.1 M potassium chloride 24% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Mar 16, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→67.94 Å / Num. obs: 39032 / % possible obs: 99.9 % / Redundancy: 23.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.019 / Net I/σ(I): 23.3 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 13.5 % / Rmerge(I) obs: 0.468 / Mean I/σ(I) obs: 5.6 / Num. unique obs: 5534 / CC1/2: 0.875 / Rpim(I) all: 0.131 / % possible all: 99.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6LDV Resolution: 1.8→67.94 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.939 / SU B: 4.958 / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.122 / ESU R Free: 0.123 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
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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 max: 66.3 Å2 / Biso mean: 21.935 Å2 / Biso min: 13.75 Å2
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Refinement step | Cycle: final / Resolution: 1.8→67.94 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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