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Yorodumi- PDB-6n3x: Human Histidine Triad Nucleotide Binding Protein 1 (Hint1) with B... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6n3x | ||||||
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Title | Human Histidine Triad Nucleotide Binding Protein 1 (Hint1) with Bound 5'-O-[1-Benzyl]Carbamoyl Guanosine | ||||||
Components | Histidine triad nucleotide-binding protein 1 | ||||||
Keywords | HYDROLASE / HINT / histidine triad / HIT | ||||||
Function / homology | Function and homology information purine ribonucleotide catabolic process / adenylylsulfatase activity / Hydrolases; Acting on phosphorus-nitrogen bonds / adenosine 5'-monophosphoramidase activity / deSUMOylase activity / protein desumoylation / sulfur compound metabolic process / histone deacetylase complex / intrinsic apoptotic signaling pathway by p53 class mediator / positive regulation of calcium-mediated signaling ...purine ribonucleotide catabolic process / adenylylsulfatase activity / Hydrolases; Acting on phosphorus-nitrogen bonds / adenosine 5'-monophosphoramidase activity / deSUMOylase activity / protein desumoylation / sulfur compound metabolic process / histone deacetylase complex / intrinsic apoptotic signaling pathway by p53 class mediator / 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: 1.1 Å | ||||||
Authors | Strom, A.M. / Finzel, B.C. | ||||||
Citation | Journal: Acs Chem Neurosci / Year: 2019 Title: Inhibition of HINT1 Modulates Spinal Nociception and NMDA Evoked Behavior in Mice. Authors: Shah, R.M. / Peterson, C. / Strom, A. / Dillenburg, M. / Finzel, B. / Kitto, K.F. / Fairbanks, C. / Wilcox, G. / 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 | 6n3x.cif.gz | 70.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6n3x.ent.gz | 49.9 KB | Display | PDB format |
PDBx/mmJSON format | 6n3x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n3/6n3x ftp://data.pdbj.org/pub/pdb/validation_reports/n3/6n3x | HTTPS FTP |
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-Related structure data
Related structure data | 6n3vC 6n3wC 6n3yC 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: 14096.188 Da / Num. of mol.: 2 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 BL21(DE3) (bacteria) / Strain (production host): Rosetta 2 pLysS BL21(DE3) / References: UniProt: P49773 #2: Chemical | ChemComp-KBD / | #3: Chemical | #4: Chemical | ChemComp-CL / | #5: 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: 2.05 Å3/Da / Density % sol: 39.88 % / Mosaicity: 0.12 ° |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 6.3 / Details: 100 mM MES, 35% PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RDI CMOS_8M / Detector: CMOS / Date: Sep 24, 2015 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.1→31.919 Å / Num. all: 90215 / Num. obs: 90215 / % possible obs: 97.7 % / Redundancy: 3.5 % / Biso Wilson estimate: 6.98 Å2 / Rpim(I) all: 0.032 / Rrim(I) all: 0.061 / Rsym value: 0.051 / Net I/av σ(I): 11.5 / Net I/σ(I): 15.7 / Num. measured all: 316410 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3TW2 Resolution: 1.1→31.919 Å / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 16.3
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 47.59 Å2 / Biso mean: 10.3596 Å2 / Biso min: 3.07 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.1→31.919 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30
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