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Yorodumi- PDB-3oc3: Crystal structure of the Mot1 N-terminal domain in complex with TBP -
+Open data
-Basic information
Entry | Database: PDB / ID: 3oc3 | ||||||
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Title | Crystal structure of the Mot1 N-terminal domain in complex with TBP | ||||||
Components |
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Keywords | HYDROLASE/TRANSCRIPTION / Transcription / Regulation of Transcription / HYDROLASE-TRANSCRIPTION complex | ||||||
Function / homology | Function and homology information ATP-dependent chromatin remodeler activity / RNA polymerase II general transcription initiation factor activity / TBP-class protein binding / helicase activity / DNA-templated transcription initiation / ATP hydrolysis activity / DNA binding / ATP binding / identical protein binding / nucleus Similarity search - Function | ||||||
Biological species | Encephalitozoon cuniculi (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.1 Å | ||||||
Authors | Wollmann, P. / Cui, S. / Viswanathan, R. / Berninghausen, O. / Wells, M.N. / Moldt, M. / Witte, G. / Butryn, A. / Wendler, P. / Beckmann, R. ...Wollmann, P. / Cui, S. / Viswanathan, R. / Berninghausen, O. / Wells, M.N. / Moldt, M. / Witte, G. / Butryn, A. / Wendler, P. / Beckmann, R. / Auble, D.T. / Hopfner, K.-P. | ||||||
Citation | Journal: Nature / Year: 2011 Title: Structure and mechanism of the Swi2/Snf2 remodeller Mot1 in complex with its substrate TBP. Authors: Wollmann, P. / Cui, S. / Viswanathan, R. / Berninghausen, O. / Wells, M.N. / Moldt, M. / Witte, G. / Butryn, A. / Wendler, P. / Beckmann, R. / Auble, D.T. / Hopfner, K.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3oc3.cif.gz | 381.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3oc3.ent.gz | 308 KB | Display | PDB format |
PDBx/mmJSON format | 3oc3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3oc3_validation.pdf.gz | 489 KB | Display | wwPDB validaton report |
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Full document | 3oc3_full_validation.pdf.gz | 551.6 KB | Display | |
Data in XML | 3oc3_validation.xml.gz | 68.8 KB | Display | |
Data in CIF | 3oc3_validation.cif.gz | 92.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oc/3oc3 ftp://data.pdbj.org/pub/pdb/validation_reports/oc/3oc3 | HTTPS FTP |
-Related 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: 91981.445 Da / Num. of mol.: 2 / Fragment: HEAT domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Encephalitozoon cuniculi (fungus) / Gene: ECU03_1530 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q8SVZ5 #2: Protein | Mass: 24502.486 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Encephalitozoon cuniculi (fungus) / Gene: ECU04_1440 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8ST28 #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: 3.26 Å3/Da / Density % sol: 62.32 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 50mM Mes pH 6, 200mM Ammoniumacetate, 5% MPD, 4% PEG 3350, 200mM NDSB-201, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 10, 2009 |
Radiation | Monochromator: Silicon 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→50 Å / Num. obs: 54019 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 3.1→3.2 Å / % possible all: 97.2 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 3.1→47.276 Å / SU ML: 0.4 / σ(F): 2 / Phase error: 24.95 / 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 / Bsol: 44.11 Å2 / ksol: 0.269 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 3.1→47.276 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 19
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