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Yorodumi- PDB-5wa9: Human Histidine Triad Nucleotide Binding Protein 1 (hHint1) H112N... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5wa9 | ||||||
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Title | Human Histidine Triad Nucleotide Binding Protein 1 (hHint1) H112N mutant nucleoside D-Ala phosphoramidate substrate complex | ||||||
Components | Histidine triad nucleotide-binding protein 1 | ||||||
Keywords | HYDROLASE / histidine triad | ||||||
Function / homology | Function and homology information purine ribonucleotide catabolic process / Hydrolases; Acting on phosphorus-nitrogen bonds / adenosine 5'-monophosphoramidase activity / deSUMOylase activity / protein desumoylation / Regulation of MITF-M-dependent genes involved in apoptosis / histone deacetylase complex / intrinsic apoptotic signaling pathway by p53 class mediator / Transcriptional and post-translational regulation of MITF-M expression and activity / positive regulation of calcium-mediated signaling ...purine ribonucleotide catabolic process / Hydrolases; Acting on phosphorus-nitrogen bonds / adenosine 5'-monophosphoramidase activity / deSUMOylase activity / protein desumoylation / Regulation of MITF-M-dependent genes involved in apoptosis / histone deacetylase complex / intrinsic apoptotic signaling pathway by p53 class mediator / Transcriptional and post-translational regulation of MITF-M expression and activity / positive regulation of calcium-mediated signaling / protein kinase C binding / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / cytoskeleton / hydrolase activity / nucleotide binding / regulation of DNA-templated transcription / signal transduction / proteolysis / extracellular exosome / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.15 Å | ||||||
Authors | Maize, K.M. / Finzel, B.C. | ||||||
Citation | Journal: Mol. Pharm. / Year: 2017 Title: A Crystal Structure Based Guide to the Design of Human Histidine Triad Nucleotide Binding Protein 1 (hHint1) Activated ProTides. Authors: Maize, K.M. / Shah, R. / Strom, A. / Kumarapperuma, S. / Zhou, A. / Wagner, C.R. / Finzel, B.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5wa9.cif.gz | 116.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5wa9.ent.gz | 87.2 KB | Display | PDB format |
PDBx/mmJSON format | 5wa9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wa/5wa9 ftp://data.pdbj.org/pub/pdb/validation_reports/wa/5wa9 | HTTPS FTP |
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-Related structure data
Related structure data | 5klyC 5klzC 5km0C 5km1C 5km2C 5km3C 5km4C 5km5C 5km6C 5km8C 5km9C 5kmaC 5kmbC 5wa8C 6b42C 3tw2S C: citing same article (ref.) S: Starting model for refinement |
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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: 14072.145 Da / Num. of mol.: 2 / Mutation: H112N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HINT1, HINT, PKCI1, PRKCNH1 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 pLysS / References: UniProt: P49773, Hydrolases #2: Chemical | ChemComp-9ZD / [( | #3: Chemical | ChemComp-CL / | #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: 2.03 Å3/Da / Density % sol: 39.46 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.7 / Details: 100 mM MES, 36% PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 19, 2017 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.15→63.989 Å / Num. obs: 76481 / % possible obs: 95.3 % / Redundancy: 3.3 % / Biso Wilson estimate: 7.25 Å2 / CC1/2: 0.931 / Rpim(I) all: 0.065 / Rrim(I) all: 0.12 / Net I/σ(I): 10.5 / Num. measured all: 252713 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3TW2 Resolution: 1.15→38.651 Å / SU ML: 0.07 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 14.23
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 43.2 Å2 / Biso mean: 12.2048 Å2 / Biso min: 5.17 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.15→38.651 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 27
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