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Yorodumi- PDB-3q7j: Engineered Thermoplasma Acidophilum F3 factor mimics human aminop... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3q7j | ||||||
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Title | Engineered Thermoplasma Acidophilum F3 factor mimics human aminopeptidase N (APN) as a target for anticancer drug development | ||||||
Components | Tricorn protease-interacting factor F3 | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / Trf3 / Inhibitor FBO / Aminopeptidase / Inhibitor binding / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | Function and homology information Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases / peptide catabolic process / metalloaminopeptidase activity / peptide binding / proteolysis / zinc ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Thermoplasma acidophilum (acidophilic) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.91 Å | ||||||
Authors | Su, J. / Wang, Q. / Feng, J. / Zhang, C. / Zhu, D. / We, T. / Xu, W. / Gu, L. | ||||||
Citation | Journal: Bioorg.Med.Chem. / Year: 2011 Title: Engineered Thermoplasma acidophilum factor F3 mimics human aminopeptidase N (APN) as a target for anticancer drug development Authors: Su, J. / Wang, Q. / Feng, J. / Zhang, C. / Zhu, D. / Wei, T. / Xu, W. / Gu, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3q7j.cif.gz | 315.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3q7j.ent.gz | 255.6 KB | Display | PDB format |
PDBx/mmJSON format | 3q7j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3q7j_validation.pdf.gz | 724 KB | Display | wwPDB validaton report |
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Full document | 3q7j_full_validation.pdf.gz | 779.1 KB | Display | |
Data in XML | 3q7j_validation.xml.gz | 58.1 KB | Display | |
Data in CIF | 3q7j_validation.cif.gz | 78.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q7/3q7j ftp://data.pdbj.org/pub/pdb/validation_reports/q7/3q7j | HTTPS FTP |
-Related structure data
Related structure data | 1z5hS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 89478.742 Da / Num. of mol.: 2 / Mutation: E101Q,N261T Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermoplasma acidophilum (acidophilic) / Strain: DSM 1728 / Gene: O93655, Ta0815, trf3 / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: O93655, Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases #2: Chemical | #3: Chemical | ChemComp-FBO / | #4: Water | ChemComp-HOH / | Compound details | THE LINK BETWEEN FBO AND ZN IS THE INHIBITOR BINDING. | |
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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: 3.09 Å3/Da / Density % sol: 60.14 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 18% PEG 2000, 0.2M LITHIUM SULPHATE, 0.1M Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å | |||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 19, 2009 | |||||||||||||||||||||
Radiation | Monochromator: SAGITTALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 | |||||||||||||||||||||
Reflection | Resolution: 2.9→50 Å / Num. all: 49142 / Num. obs: 49142 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Biso Wilson estimate: 49.9 Å2 / Rmerge(I) obs: 0.128 / Rsym value: 0.128 / Net I/σ(I): 16.14 | |||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1Z5H Resolution: 2.91→47.953 Å / SU ML: 0.35 / σ(F): 0 / σ(I): 0 / Phase error: 27.13 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 20 Å2 / ksol: 0.313 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 52.007 Å2
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Refinement step | Cycle: LAST / Resolution: 2.91→47.953 Å
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Refine LS restraints |
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LS refinement shell |
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