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- PDB-6yqm: Human histidine triad nucleotide-binding protein 1 (hHINT1) compl... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6yqm | ||||||
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Title | Human histidine triad nucleotide-binding protein 1 (hHINT1) complexed with dGMP and refined to 1.02 A | ||||||
![]() | Histidine triad nucleotide-binding protein 1 | ||||||
![]() | HYDROLASE / Nucleotide binding protein | ||||||
Function / homology | ![]() 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 / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Dolot, R.D. / Seda, A. / Nawrot, B.C. | ||||||
![]() | ![]() Title: Biochemical, crystallographic and biophysical characterization of histidine triad nucleotide-binding protein 2 with different ligands including a non-hydrolyzable analog of Ap4A. Authors: Dolot, R. / Krakowiak, A. / Kaczmarek, R. / Wlodarczyk, A. / Pichlak, M. / Nawrot, B. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 133.3 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 18.5 KB | Display | |
Data in CIF | ![]() | 28.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6yi0C ![]() 6yprC ![]() 6ypxC ![]() 6yqdC ![]() 6yvpC ![]() 3tw2S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 13823.931 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-DGP / | #3: Chemical | ChemComp-PEG / | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 46.83 % |
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Crystal grow | Temperature: 281 K / Method: vapor diffusion, hanging drop / pH: 5.7 / Details: 16 % (w/v) PEG 4000, 0.1 M sodium cacodylate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Mar 7, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 1.02→39.963 Å / Num. obs: 116020 / % possible obs: 99.1 % / Redundancy: 3.8 % / Biso Wilson estimate: 5.1 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.042 / Rpim(I) all: 0.037 / Rrim(I) all: 0.056 / Χ2: 1.04 / Net I/σ(I): 14.1 |
Reflection shell | Resolution: 1.02→1.04 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.466 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 5440 / CC1/2: 0.785 / Rpim(I) all: 0.422 / Rrim(I) all: 0.63 / Χ2: 1.06 / % possible all: 93.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3TW2 Resolution: 1.02→39.96 Å / Cor.coef. Fo:Fc: 0.984 / Cor.coef. Fo:Fc free: 0.977 / SU B: 0.678 / SU ML: 0.015 / Cross valid method: THROUGHOUT / ESU R: 0.02 / ESU R Free: 0.022 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 11.705 Å2
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Refinement step | Cycle: LAST / Resolution: 1.02→39.96 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: 20
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