+Open data
-Basic information
Entry | Database: PDB / ID: 5ed3 | |||||||||
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Title | crystal structure of human Hint1 complexing with AP5A | |||||||||
Components | Histidine triad nucleotide-binding protein 1 | |||||||||
Keywords | HYDROLASE / nucleotide binding / regulation of transcription / signal transduction | |||||||||
Function / homology | Function and homology information purine ribonucleotide catabolic process / Hydrolases; Acting on phosphorus-nitrogen bonds / adenosine 5'-monophosphoramidase activity / deSUMOylase activity / protein desumoylation / 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 ...purine ribonucleotide catabolic process / Hydrolases; Acting on phosphorus-nitrogen bonds / adenosine 5'-monophosphoramidase activity / deSUMOylase activity / protein desumoylation / 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: 1.309 Å | |||||||||
Authors | Wang, J. / Fang, P. / Guo, M. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Nat Commun / Year: 2019 Title: Second messenger Ap4A polymerizes target protein HINT1 to transduce signals in Fc epsilon RI-activated mast cells. Authors: Yu, J. / Liu, Z. / Liang, Y. / Luo, F. / Zhang, J. / Tian, C. / Motzik, A. / Zheng, M. / Kang, J. / Zhong, G. / Liu, C. / Fang, P. / Guo, M. / Razin, E. / Wang, J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ed3.cif.gz | 116.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ed3.ent.gz | 87.4 KB | Display | PDB format |
PDBx/mmJSON format | 5ed3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ed/5ed3 ftp://data.pdbj.org/pub/pdb/validation_reports/ed/5ed3 | HTTPS FTP |
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-Related structure data
Related structure data | 5ed6C 6j53C 6j58C 6j5sC 6j5zC 6j64C 6j65C 4eqeS 5ecb 5ecz 5ed5 5efl 5efp 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 14024.165 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HINT1, HINT, PKCI1, PRKCNH1 / Production host: Escherichia coli (E. coli) / References: UniProt: P49773, Hydrolases #2: Chemical | ChemComp-AMP / | #3: Chemical | ChemComp-EPE / | #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: 2.07 Å3/Da / Density % sol: 40.52 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: PEG3350, HEPES |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 6, 2011 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97857 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.309→25 Å / Num. obs: 55250 / % possible obs: 99.9 % / Redundancy: 7.3 % / Biso Wilson estimate: 14.77 Å2 / Rmerge(I) obs: 0.049 / Χ2: 0.952 / Net I/av σ(I): 34.675 / Net I/σ(I): 13.8 / Num. measured all: 402430 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4EQE Resolution: 1.309→24.401 Å / SU ML: 0.09 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 15.59 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.6 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 63.2 Å2 / Biso mean: 19.6974 Å2 / Biso min: 9.61 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.309→24.401 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: 19
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Refinement TLS params. | Method: refined / Origin x: 12.8569 Å / Origin y: 1.0329 Å / Origin z: 16.2614 Å
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Refinement TLS group |
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