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Yorodumi- PDB-5kcg: Crystal structure of the aromatic prenyltransferase AtaPT (apo st... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5kcg | ||||||||||||
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Title | Crystal structure of the aromatic prenyltransferase AtaPT (apo state) from Aspergillus terreus A8-4 | ||||||||||||
Components | aromatic prenyltransferase | ||||||||||||
Keywords | TRANSFERASE / aromatic prenyltransferase / ABBA fold | ||||||||||||
Function / homology | Aromatic prenyltransferase DMATS-type, fungi / Aromatic prenyltransferase, DMATS-type / Tryptophan dimethylallyltransferase / Aromatic prenyltransferase / alkaloid metabolic process / transferase activity, transferring alkyl or aryl (other than methyl) groups / Aromatic prenyltransferase Function and homology information | ||||||||||||
Biological species | Aspergillus terreus (mold) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 | 5kcg.cif.gz | 171.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5kcg.ent.gz | 134.6 KB | Display | PDB format |
PDBx/mmJSON format | 5kcg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kc/5kcg ftp://data.pdbj.org/pub/pdb/validation_reports/kc/5kcg | HTTPS FTP |
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-Related structure data
Related structure data | 5kclC 5kcqC 5kcyC 5kd0C 5kd6C 5kdaC 3i4zS 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / 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: 0 / 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 Source: (gene. exp.) Aspergillus terreus (mold) / Strain: A8-4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A1B0UHJ4*PLUS #2: 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: 2.46 Å3/Da / Density % sol: 49.99 % |
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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: 0.97 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 20, 2013 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.9→135.81 Å / Num. all: 71707 / Num. obs: 71707 / % possible obs: 99.1 % / Redundancy: 4.9 % / Rpim(I) all: 0.043 / Rrim(I) all: 0.098 / Rsym value: 0.088 / Net I/av σ(I): 5.417 / Net I/σ(I): 11.1 / Num. measured all: 354138 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3I4Z Resolution: 1.9→48.58 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.926 / SU B: 3.637 / SU ML: 0.105 / Cross valid method: THROUGHOUT / ESU R: 0.147 / ESU R Free: 0.142 / 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: 30.338 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→48.58 Å
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Refine LS restraints |
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