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Yorodumi- PDB-2ome: Crystal structure of human CTBP2 dehydrogenase complexed with NAD(H) -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ome | ||||||
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Title | Crystal structure of human CTBP2 dehydrogenase complexed with NAD(H) | ||||||
Components | C-terminal-binding protein 2 | ||||||
Keywords | OXIDOREDUCTASE / C-TERMINAL BINDING PROTEIN / CTBP2 / DEHYDROGENASE / STRUCTURAL GENOMICS CONSORTIUM / SGC | ||||||
Function / homology | Function and homology information positive regulation of retinoic acid receptor signaling pathway / Signaling by TCF7L2 mutants / Repression of WNT target genes / Sensory processing of sound by inner hair cells of the cochlea / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / white fat cell differentiation / transcription repressor complex / viral genome replication / transcription corepressor binding / transcription coregulator binding ...positive regulation of retinoic acid receptor signaling pathway / Signaling by TCF7L2 mutants / Repression of WNT target genes / Sensory processing of sound by inner hair cells of the cochlea / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / white fat cell differentiation / transcription repressor complex / viral genome replication / transcription corepressor binding / transcription coregulator binding / transcription corepressor activity / NAD binding / DNA-binding transcription factor binding / transcription coactivator activity / negative regulation of cell population proliferation / negative regulation of DNA-templated transcription / synapse / protein-containing complex binding / regulation of transcription by RNA polymerase II / protein kinase binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / identical protein binding / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Pilka, E.S. / Guo, K. / Rojkova, A. / Debreczeni, J.E. / Kavanagh, K.L. / von Delft, F. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. / Sundstrom, M. ...Pilka, E.S. / Guo, K. / Rojkova, A. / Debreczeni, J.E. / Kavanagh, K.L. / von Delft, F. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. / Sundstrom, M. / Oppermann, U. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: To be Published Title: Crystal structure of human CTBP2 dehydrogenase complexed with NAD(H) Authors: Pilka, E.S. / Guo, K. / Rojkova, A. / Debreczeni, J.E. / Kavanagh, K.L. / von Delft, F. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. / Sundstrom, M. / Oppermann, U. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ome.cif.gz | 492.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ome.ent.gz | 406.8 KB | Display | PDB format |
PDBx/mmJSON format | 2ome.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2ome_validation.pdf.gz | 2.8 MB | Display | wwPDB validaton report |
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Full document | 2ome_full_validation.pdf.gz | 2.8 MB | Display | |
Data in XML | 2ome_validation.xml.gz | 92.2 KB | Display | |
Data in CIF | 2ome_validation.cif.gz | 122.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/om/2ome ftp://data.pdbj.org/pub/pdb/validation_reports/om/2ome | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: PHE / End label comp-ID: PHE / Refine code: 3 / Auth seq-ID: 34 - 362 / Label seq-ID: 6 - 334
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-Components
#1: Protein | Mass: 37274.477 Da / Num. of mol.: 8 / Fragment: Residues 31-364 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CTBP2 / Plasmid: pNIC28-Bsa4 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P56545 #2: Chemical | ChemComp-NAD / #3: 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: 2.84 Å3/Da / Density % sol: 56.74 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.2M KSCN, 0.1M BIS-TRIS PROPANE, 20% PEG3350, 10% ETHYLENE GLYCOL, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99991 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 21, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99991 Å / Relative weight: 1 |
Reflection | Resolution: 2.77→43.31 Å / Num. obs: 84796 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 6.1 % / Rmerge(I) obs: 0.148 / Rsym value: 0.162 / Net I/σ(I): 11.6 |
Reflection shell | Resolution: 2.77→2.92 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.81 / Mean I/σ(I) obs: 2 / Rsym value: 0.89 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entries 1MX3, 1HL3 Resolution: 2.8→43.31 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.9 / SU B: 30.465 / SU ML: 0.3 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R Free: 0.378 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.724 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→43.31 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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