+Open data
-Basic information
Entry | Database: PDB / ID: 6ldv | ||||||
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Title | Structure antibody F9 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 / protein serine kinase activity / protein serine/threonine kinase activity / protein kinase binding / nucleoplasm / ATP binding ...mitogen-activated protein kinase kinase kinase / MAP kinase kinase kinase activity / cellular response to mechanical stimulus / protein kinase activity / intracellular signal transduction / protein serine kinase activity / protein serine/threonine kinase activity / protein kinase binding / nucleoplasm / ATP binding / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Oryctolagus cuniculus (rabbit) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 | 6ldv.cif.gz | 104.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ldv.ent.gz | 76.7 KB | Display | PDB format |
PDBx/mmJSON format | 6ldv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ldv_validation.pdf.gz | 446.5 KB | Display | wwPDB validaton report |
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Full document | 6ldv_full_validation.pdf.gz | 447.7 KB | Display | |
Data in XML | 6ldv_validation.xml.gz | 21.2 KB | Display | |
Data in CIF | 6ldv_validation.cif.gz | 31.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ld/6ldv ftp://data.pdbj.org/pub/pdb/validation_reports/ld/6ldv | HTTPS FTP |
-Related structure data
Related structure data | 6ldwC 6ldxC 6ldyC 5m63S 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
#1: Antibody | Mass: 25532.479 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Cell line (production host): 293 / Production host: Homo sapiens (human) | ||||
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#2: Antibody | Mass: 25301.645 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-IOD / #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: 1.93 Å3/Da / Density % sol: 36.25 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: 0.2 M potassium iodide 20% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å |
Detector | Type: RAYONIX MX225-HS / Detector: CCD / Date: Aug 5, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→46.32 Å / Num. obs: 31867 / % possible obs: 99.2 % / Redundancy: 14.4 % / CC1/2: 0.997 / Rmerge(I) obs: 0.193 / Rpim(I) all: 0.052 / Net I/σ(I): 14.1 |
Reflection shell | Resolution: 1.9→1.95 Å / Rmerge(I) obs: 1.213 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1856 / CC1/2: 0.677 / Rpim(I) all: 0.379 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5M63 Resolution: 1.9→46.32 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.926 / SU B: 4.033 / SU ML: 0.114 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.162 / ESU R Free: 0.151 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY 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: 78.35 Å2 / Biso mean: 19.912 Å2 / Biso min: 10.81 Å2
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Refinement step | Cycle: final / Resolution: 1.9→46.32 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.902→1.951 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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