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Yorodumi- PDB-6a0f: Crystal structure of human protein N-terminal asparagine amidohyd... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6a0f | |||||||||
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Title | Crystal structure of human protein N-terminal asparagine amidohydrolase (NTAN1) C75S mutant with Asn-Phe-Ala-Ala-Arg peptide | |||||||||
Components |
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Keywords | HYDROLASE / Complex / Amidohydrolase | |||||||||
Function / homology | Function and homology information protein N-terminal asparagine amidohydrolase / protein-N-terminal asparagine amidohydrolase activity / adult locomotory behavior / memory / ubiquitin-dependent protein catabolic process / nucleus / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) synthetic construct (others) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.384 Å | |||||||||
Authors | Park, J.S. / Han, B.W. | |||||||||
Funding support | Korea, Republic Of, 2items
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Citation | Journal: Biomolecules / Year: 2020 Title: Structural Analyses on the Deamidation of N-Terminal Asn in the Human N-Degron Pathway. Authors: Park, J.S. / Lee, J.Y. / Nguyen, Y.T.K. / Kang, N.W. / Oh, E.K. / Jang, D.M. / Kim, H.J. / Kim, D.D. / Han, B.W. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6a0f.cif.gz | 143.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6a0f.ent.gz | 110.7 KB | Display | PDB format |
PDBx/mmJSON format | 6a0f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a0/6a0f ftp://data.pdbj.org/pub/pdb/validation_reports/a0/6a0f | HTTPS FTP |
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-Related structure data
Related structure data | 6a0eC 6a0hC 6a0iSC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 35778.227 Da / Num. of mol.: 2 / Mutation: C75S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NTAN1 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 References: UniProt: Q96AB6, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides #2: Protein/peptide | Mass: 578.641 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-PO4 / #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: 2.19 Å3/Da / Density % sol: 43.78 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.8 / Details: PEG 3350, potassium phosphate monobasic |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: Liquid nitrogen flow / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97933 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Sep 17, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97933 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. obs: 25940 / % possible obs: 99.9 % / Redundancy: 7.8 % / Rpim(I) all: 0.035 / Rsym value: 0.092 / Net I/σ(I): 18.41 |
Reflection shell | Resolution: 2.4→2.44 Å / Num. unique obs: 1246 / Rpim(I) all: 0.19 / Rsym value: 0.502 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6A0I Resolution: 2.384→30.757 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.23 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.384→30.757 Å
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Refine LS restraints |
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LS refinement shell |
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