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Yorodumi- PDB-5kcl: Crystal structure of the aromatic prenyltransferase AtaPT from As... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5kcl | ||||||||||||
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Title | Crystal structure of the aromatic prenyltransferase AtaPT from Aspergillus terreus A8-4 in complex with dimethylallyl S-thiolodiphosphate | ||||||||||||
Components | aromatic prenyltransferase | ||||||||||||
Keywords | TRANSFERASE / substrate promiscuity / ABBA fold | ||||||||||||
Function / homology | Aromatic prenyltransferase DMATS-type, fungi / Aromatic prenyltransferase, DMATS-type / Tryptophan dimethylallyltransferase / Aromatic prenyltransferase / transferase activity, transferring alkyl or aryl (other than methyl) groups / alkaloid metabolic process / DIMETHYLALLYL S-THIOLODIPHOSPHATE / Aromatic prenyltransferase Function and homology information | ||||||||||||
Biological species | Aspergillus terreus (mold) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||||||||
Authors | Sun, F. / Gao, B. | ||||||||||||
Funding support | China, 3items
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Citation | Journal: Nat. Chem. Biol. / Year: 2017 Title: Molecular insights into the enzyme promiscuity of an aromatic prenyltransferase. Authors: Chen, R. / Gao, B. / Liu, X. / Ruan, F. / Zhang, Y. / Lou, J. / Feng, K. / Wunsch, C. / Li, S.M. / Dai, J. / Sun, F. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5kcl.cif.gz | 173.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5kcl.ent.gz | 135.9 KB | Display | PDB format |
PDBx/mmJSON format | 5kcl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kc/5kcl ftp://data.pdbj.org/pub/pdb/validation_reports/kc/5kcl | HTTPS FTP |
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-Related structure data
Related structure data | 5kcgSC 5kcqC 5kcyC 5kd0C 5kd6C 5kdaC 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ARG / Beg label comp-ID: ARG / End auth comp-ID: VAL / End label comp-ID: VAL / Refine code: _ / Auth seq-ID: 11 - 421 / Label seq-ID: 6 - 416
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-Components
#1: Protein | Mass: 46895.770 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Dimethylallyl S-Thiolodiphosphate / Source: (gene. exp.) Aspergillus terreus (mold) / Strain: A8-4 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1B0UHJ4*PLUS #2: Chemical | #3: 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: 2.37 Å3/Da / Density % sol: 48.2 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 25 mM Bis-Tris, pH 6.0, 0.2 M (NH4)2SO4, 17% PEG 3350, 3.3% DDM |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97907 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 25, 2013 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97907 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.1→132.97 Å / Num. obs: 51286 / % possible obs: 98.6 % / Redundancy: 4.9 % / Rsym value: 0.077 / Net I/av σ(I): 7.236 / Net I/σ(I): 12.9 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5KCG Resolution: 2.1→132.97 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.921 / SU B: 4.877 / SU ML: 0.13 / Cross valid method: THROUGHOUT / ESU R: 0.226 / ESU R Free: 0.184 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.783 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→132.97 Å
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Refine LS restraints |
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