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Yorodumi- PDB-6a0e: Crystal structure of human protein N-terminal asparagine amidohyd... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6a0e | |||||||||
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Title | Crystal structure of human protein N-terminal asparagine amidohydrolase (NTAN1) | |||||||||
Components | Protein N-terminal asparagine amidohydrolase | |||||||||
Keywords | HYDROLASE / 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) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.947 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 | 6a0e.cif.gz | 148.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6a0e.ent.gz | 121.7 KB | Display | PDB format |
PDBx/mmJSON format | 6a0e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6a0e_validation.pdf.gz | 465.5 KB | Display | wwPDB validaton report |
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Full document | 6a0e_full_validation.pdf.gz | 478 KB | Display | |
Data in XML | 6a0e_validation.xml.gz | 31.9 KB | Display | |
Data in CIF | 6a0e_validation.cif.gz | 46.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a0/6a0e ftp://data.pdbj.org/pub/pdb/validation_reports/a0/6a0e | HTTPS FTP |
-Related 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: 35794.293 Da / Num. of mol.: 2 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: Chemical | ChemComp-GOL / #3: Chemical | ChemComp-PO4 / | #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: 2.15 Å3/Da / Density % sol: 42.79 % / Description: Rod-shaped |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.8 / Details: PEG 3350, Potassium phosphate monobasic / Temp details: incubator |
-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: 5C (4A) / Wavelength: 0.9796 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 11, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9796 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→50 Å / Num. obs: 45885 / % possible obs: 100 % / Redundancy: 7.3 % / Rpim(I) all: 0.037 / Rsym value: 0.091 / Net I/σ(I): 21.18 |
Reflection shell | Resolution: 1.95→1.98 Å / Redundancy: 7.3 % / Num. unique obs: 2264 / Rpim(I) all: 0.276 / Rsym value: 0.701 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.947→30.415 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.11 / 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: 1.947→30.415 Å
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Refine LS restraints |
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LS refinement shell |
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