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Yorodumi- PDB-5k8p: Zn2+/Tetrahedral intermediate-bound R289A 5-nitroanthranilate ami... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5k8p | ||||||
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Title | Zn2+/Tetrahedral intermediate-bound R289A 5-nitroanthranilate aminohydrolase | ||||||
Components | 5-nitroanthranilic acid aminohydrolase | ||||||
Keywords | HYDROLASE / Nitroaromatics / deaminase / metalloenzyme | ||||||
Function / homology | Function and homology information 5-nitroanthranilic acid aminohydrolase / hydrolase activity / metal ion binding Similarity search - Function | ||||||
Biological species | Bradyrhizobium sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Kalyoncu, S. | ||||||
Citation | Journal: Nat.Chem.Biol. / Year: 2016 Title: Enzymatic hydrolysis by transition-metal-dependent nucleophilic aromatic substitution. Authors: Kalyoncu, S. / Heaner, D.P. / Kurt, Z. / Bethel, C.M. / Ukachukwu, C.U. / Chakravarthy, S. / Spain, J.C. / Lieberman, R.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5k8p.cif.gz | 678.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5k8p.ent.gz | 556.4 KB | Display | PDB format |
PDBx/mmJSON format | 5k8p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k8/5k8p ftp://data.pdbj.org/pub/pdb/validation_reports/k8/5k8p | HTTPS FTP |
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-Related structure data
Related structure data | 5k8mC 5k8nC 5k8oSC 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: 46314.438 Da / Num. of mol.: 8 / Mutation: R289A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bradyrhizobium sp. (bacteria) / Gene: naaA / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 (DE3) References: UniProt: D3WZ85, 5-nitroanthranilic acid aminohydrolase #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-6R8 / ( #4: Chemical | ChemComp-GOL / #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: 3.85 Å3/Da / Density % sol: 68.05 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 0.1 M sodium cacodylate pH 6.5, 0.65 M trisodium citrate, 12 mM zinc acetate, 0.22 mM 5-nitroanthranilic acid |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 22, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→37.16 Å / Num. obs: 337936 / % possible obs: 98.31 % / Redundancy: 5.7 % / Net I/σ(I): 14.63 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5K8O Resolution: 2.2→37.16 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.67
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→37.16 Å
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Refine LS restraints |
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LS refinement shell |
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