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Yorodumi- PDB-5ipb: Human Histidine Triad Nucleotide Binding Protein 1 (hHint1) H112N... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ipb | ||||||
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Title | Human Histidine Triad Nucleotide Binding Protein 1 (hHint1) H112N mutant | ||||||
Components | Histidine triad nucleotide-binding protein 1 | ||||||
Keywords | HYDROLASE / HINT / histidine triad / HIT | ||||||
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 / Resolution: 1.55 Å | ||||||
Authors | Maize, K.M. / Finzel, B.C. | ||||||
Citation | Journal: Biochemistry / Year: 2017 Title: Caught before Released: Structural Mapping of the Reaction Trajectory for the Sofosbuvir Activating Enzyme, Human Histidine Triad Nucleotide Binding Protein 1 (hHint1). Authors: Shah, R. / Maize, K.M. / Zhou, X. / Finzel, B.C. / Wagner, C.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ipb.cif.gz | 64.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ipb.ent.gz | 45.1 KB | Display | PDB format |
PDBx/mmJSON format | 5ipb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ip/5ipb ftp://data.pdbj.org/pub/pdb/validation_reports/ip/5ipb | HTTPS FTP |
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-Related structure data
Related structure data | 5ipcC 5ipdC 5ipeC 3tw2S 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: 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 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 pLysS / References: UniProt: P49773, Hydrolases #2: Chemical | #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: 2.21 Å3/Da / Density % sol: 44.38 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 6.7 / Details: 100 mM MES, 33% 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: Apr 18, 2015 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.55→34.824 Å / Num. obs: 33064 / % possible obs: 97.8 % / Redundancy: 3.1 % / Biso Wilson estimate: 13.01 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.034 / Rrim(I) all: 0.062 / Net I/σ(I): 14 / Num. measured all: 102047 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3TW2 Resolution: 1.55→34.824 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 20.12 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 55.06 Å2 / Biso mean: 16.3009 Å2 / Biso min: 6.45 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.55→34.824 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: 12
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