+Open data
-Basic information
Entry | Database: PDB / ID: 2h2h | ||||||
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Title | The Structural basis of sirtuin substrate specificity | ||||||
Components |
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Keywords | HYDROLASE / H4-K79ac | ||||||
Function / homology | Function and homology information HDMs demethylate histones / HATs acetylate histones / RNA polymerase I upstream activating factor complex / Condensation of Prophase Chromosomes / protein acetyllysine N-acetyltransferase / SUMOylation of chromatin organization proteins / NAD-dependent histone deacetylase activity / replication fork protection complex / RMTs methylate histone arginines / positive regulation of transcription by RNA polymerase I ...HDMs demethylate histones / HATs acetylate histones / RNA polymerase I upstream activating factor complex / Condensation of Prophase Chromosomes / protein acetyllysine N-acetyltransferase / SUMOylation of chromatin organization proteins / NAD-dependent histone deacetylase activity / replication fork protection complex / RMTs methylate histone arginines / positive regulation of transcription by RNA polymerase I / nucleolar large rRNA transcription by RNA polymerase I / NAD+ binding / structural constituent of chromatin / nucleosome / nucleosome assembly / chromatin organization / transferase activity / protein heterodimerization activity / regulation of DNA-templated transcription / DNA binding / zinc ion binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Thermotoga maritima (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Cosgrove, M.S. / Wolberger, C. | ||||||
Citation | Journal: Biochemistry / Year: 2006 Title: The structural basis of sirtuin substrate affinity Authors: Cosgrove, M.S. / Bever, K. / Avalos, J.L. / Muhammad, S. / Zhang, X. / Wolberger, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2h2h.cif.gz | 64.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2h2h.ent.gz | 46 KB | Display | PDB format |
PDBx/mmJSON format | 2h2h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h2/2h2h ftp://data.pdbj.org/pub/pdb/validation_reports/h2/2h2h | HTTPS FTP |
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-Related structure data
Related structure data | 2h2dC 2h2fC 2h2gC 2h2iSC 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
#1: Protein | Mass: 27569.793 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: npdA / Production host: Escherichia coli (E. coli) References: UniProt: Q9WYW0, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides |
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#2: Protein/peptide | Mass: 1300.484 Da / Num. of mol.: 1 / Source method: obtained synthetically / References: UniProt: P02309 |
#3: Chemical | ChemComp-ZN / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.73 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 9.5 Details: 20 % PEG, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K, pH 9.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-D / Wavelength: 1 Å |
Detector | Detector: CCD / Date: Dec 5, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. all: 3 / Num. obs: 20553 / % possible obs: 98.4 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 2 / Redundancy: 4.5 % / Biso Wilson estimate: 13.1 Å2 / Rmerge(I) obs: 0.071 / Rsym value: 0.045 / Net I/σ(I): 28.1 |
Reflection shell | Resolution: 1.98→2.05 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.401 / Mean I/σ(I) obs: 5.3 / Rsym value: 0.315 / % possible all: 97.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB Entry: 2H2I Resolution: 2.2→7.98 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1514470.88 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 71.4798 Å2 / ksol: 0.560299 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→7.98 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.33 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
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Xplor file |
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