+Open data
-Basic information
Entry | Database: PDB / ID: 2jit | ||||||
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Title | Crystal structure of EGFR kinase domain T790M mutation | ||||||
Components | EPIDERMAL GROWTH FACTOR RECEPTOR | ||||||
Keywords | TRANSFERASE / EGFR / T790M / KINASE / RECEPTOR / CELL CYCLE / PHOSPHORYLATION / DISEASE MUTATION / NUCLEOTIDE-BINDING / TYROSINE-PROTEIN KINASE / ANTI-ONCOGENE / EPIDERMAL GROWTH FACTOR / ATP-BINDING | ||||||
Function / homology | Function and homology information Complex I biogenesis / Respiratory electron transport / : / mitochondrial electron transport, NADH to ubiquinone / proton motive force-driven mitochondrial ATP synthesis / NADH dehydrogenase (ubiquinone) activity / aerobic respiration / electron transfer activity / mitochondrial inner membrane Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å | ||||||
Authors | Yun, C.-H. / Mengwasser, K.E. / Toms, A.V. / Woo, M.S. / Greulich, H. / Wong, K.-K. / Meyerson, M. / Eck, M.J. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2008 Title: The T790M Mutation in Egfr Kinase Causes Drug Resistance by Increasing the Affinity for ATP. Authors: Yun, C.-H. / Mengwasser, K.E. / Toms, A.V. / Woo, M.S. / Greulich, H. / Wong, K. / Meyerson, M. / Eck, M.J. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: AUTHOR PROVIDED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2jit.cif.gz | 132.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2jit.ent.gz | 103.8 KB | Display | PDB format |
PDBx/mmJSON format | 2jit.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2jit_validation.pdf.gz | 446.4 KB | Display | wwPDB validaton report |
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Full document | 2jit_full_validation.pdf.gz | 475.7 KB | Display | |
Data in XML | 2jit_validation.xml.gz | 27.3 KB | Display | |
Data in CIF | 2jit_validation.cif.gz | 36.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ji/2jit ftp://data.pdbj.org/pub/pdb/validation_reports/ji/2jit | HTTPS FTP |
-Related structure data
Related structure data | 2jiuC 2jivC 2itnS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 37334.219 Da / Num. of mol.: 2 / Fragment: KINASE DOMAIN, RESIDUES 696-1022 / Mutation: YES Source method: isolated from a genetically manipulated source Details: EGFR 696-1022 T790M / Source: (gene. exp.) HOMO SAPIENS (human) / Description: EGFR 696-1022 T790M / Plasmid: PACG2T / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: P00533, EC: 2.7.1.112 #2: Water | ChemComp-HOH / | Compound details | ENGINEERED | Sequence details | T790M MUTATION | |
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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: 2.4 Å3/Da / Density % sol: 48 % / Description: NONE |
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Crystal grow | pH: 7.5 / Details: 0.1M HEPES 7.5, 0.3M NACL, 21% PEG6K, 5MM TCEP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97924 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Feb 15, 2007 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97924 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→50 Å / Num. obs: 16223 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 9.1 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 24 |
Reflection shell | Resolution: 3.1→3.34 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 5.5 / % possible all: 96.1 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2ITN Resolution: 3.1→24.42 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.893 / Cross valid method: THROUGHOUT / ESU R Free: 0.458 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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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: 49 Å2
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Refinement step | Cycle: LAST / Resolution: 3.1→24.42 Å
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Refine LS restraints |
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