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Yorodumi- PDB-7b10: Crystal structure of MLLT1 YEATS domain T1 mutant in complex with... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7b10 | ||||||
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Title | Crystal structure of MLLT1 YEATS domain T1 mutant in complex with benzimidazole-amide based compound 1 | ||||||
Components | Protein ENL | ||||||
Keywords | TRANSCRIPTION / T1 mutant / Structural Genomics / Structural Genomics Consortium / SGC | ||||||
Function / homology | Function and homology information RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / lysine-acetylated histone binding / RNA Polymerase II Pre-transcription Events / transcription elongation factor complex / fibrillar center / chromatin binding / positive regulation of DNA-templated transcription / nucleoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å | ||||||
Authors | Chaikuad, A. / Ni, X. / Brennan, P.E. / Knapp, S. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: Acs Chem.Biol. / Year: 2021 Title: Structure and Inhibitor Binding Characterization of Oncogenic MLLT1 Mutants. Authors: Ni, X. / Londregan, A.T. / Owen, D.R. / Knapp, S. / Chaikuad, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7b10.cif.gz | 78.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7b10.ent.gz | 57.2 KB | Display | PDB format |
PDBx/mmJSON format | 7b10.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7b10_validation.pdf.gz | 852.5 KB | Display | wwPDB validaton report |
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Full document | 7b10_full_validation.pdf.gz | 853 KB | Display | |
Data in XML | 7b10_validation.xml.gz | 8.8 KB | Display | |
Data in CIF | 7b10_validation.cif.gz | 11.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b1/7b10 ftp://data.pdbj.org/pub/pdb/validation_reports/b1/7b10 | HTTPS FTP |
-Related structure data
Related structure data | 7b0tC 6t1lS 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: Protein | Mass: 18590.410 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MLLT1, ENL, LTG19, YEATS1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q03111 | ||||
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#2: Chemical | ChemComp-GKT / | ||||
#3: Chemical | ChemComp-IOD / | ||||
#4: Chemical | ChemComp-EDO / #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: 2.08 Å3/Da / Density % sol: 40.95 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 25% w/v PEG 3350, 0.1M Bis-Tris, pH 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å | |||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 7, 2020 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 1.92→43.2 Å / Num. obs: 11770 / % possible obs: 99.2 % / Redundancy: 3.8 % / CC1/2: 0.996 / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.046 / Rrim(I) all: 0.092 / Net I/σ(I): 7.9 / Num. measured all: 45110 / Scaling rejects: 41 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / % possible all: 99.8
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6T1L Resolution: 1.92→43.2 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.958 / SU B: 8.586 / SU ML: 0.122 / SU R Cruickshank DPI: 0.1627 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.163 / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: U VALUES : WITH TLS ADDED 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 max: 83.28 Å2 / Biso mean: 39.477 Å2 / Biso min: 23.09 Å2
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Refinement step | Cycle: final / Resolution: 1.92→43.2 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.92→1.97 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: -3.1374 Å / Origin y: 12.0201 Å / Origin z: 22.4264 Å
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