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Yorodumi- PDB-5kda: Crystal structure of the aromatic prenyltransferase AtaPT from As... -
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-Basic information
Entry | Database: PDB / ID: 5kda | ||||||||||||
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Title | Crystal structure of the aromatic prenyltransferase AtaPT from Aspergillus terreus A8-4 in complex with dimethylallyl S-thiolodiphosphate and genistein | ||||||||||||
Components | aromatic prenyltransferase | ||||||||||||
Keywords | TRANSFERASE / aromatic prenyltransferase / 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 / GENISTEIN / Aromatic prenyltransferase Function and homology information | ||||||||||||
Biological species | Aspergillus terreus (mold) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 | 5kda.cif.gz | 178.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5kda.ent.gz | 140.2 KB | Display | PDB format |
PDBx/mmJSON format | 5kda.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5kda_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 5kda_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 5kda_validation.xml.gz | 34.2 KB | Display | |
Data in CIF | 5kda_validation.cif.gz | 49.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kd/5kda ftp://data.pdbj.org/pub/pdb/validation_reports/kd/5kda | HTTPS FTP |
-Related structure data
Related structure data | 5kcgSC 5kclC 5kcqC 5kcyC 5kd0C 5kd6C 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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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 46895.770 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aspergillus terreus (mold) / Strain: A8-4 / Gene: ATEG_04999 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A1B0UHJ4*PLUS #2: Chemical | ChemComp-GEN / | #3: Chemical | #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: 2.5 Å3/Da / Density % sol: 50.88 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 0.1 M 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: 0.99999 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 8, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99999 Å / Relative weight: 1 |
Reflection | Resolution: 2→78.8 Å / Num. obs: 52312 / % possible obs: 88.9 % / Redundancy: 4.2 % / Net I/σ(I): 7 |
Reflection shell | Resolution: 2→2.11 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5KCG Resolution: 2→78.8 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.916 / SU B: 4.224 / SU ML: 0.118 / Cross valid method: THROUGHOUT / ESU R: 0.207 / ESU R Free: 0.181 / 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: 26.121 Å2
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Refinement step | Cycle: 1 / Resolution: 2→78.8 Å
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Refine LS restraints |
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