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Yorodumi- PDB-6os6: Crystal structure of CymD prenyltransferase complexed with L-tryp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6os6 | |||||||||
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Title | Crystal structure of CymD prenyltransferase complexed with L-tryptophan and DMSPP | |||||||||
Components | CymD prenyltransferase | |||||||||
Keywords | TRANSFERASE / prenyltransferase / tryptophan / indole / biosynthesis | |||||||||
Function / homology | Aromatic prenyltransferase, DMATS-type / Tryptophan dimethylallyltransferase / Aromatic prenyltransferase / alkaloid metabolic process / transferase activity, transferring alkyl or aryl (other than methyl) groups / BENZOIC ACID / DIMETHYLALLYL S-THIOLODIPHOSPHATE / TRYPTOPHAN / Aromatic prenyltransferase, DMATS type Function and homology information | |||||||||
Biological species | Salinispora arenicola (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.33 Å | |||||||||
Authors | Roose, B.W. / Christianson, D.W. | |||||||||
Funding support | United States, 1items
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Citation | Journal: Biochemistry / Year: 2019 Title: Structural Basis of Tryptophan Reverse N-Prenylation Catalyzed by CymD. Authors: Roose, B.W. / Christianson, D.W. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6os6.cif.gz | 166.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6os6.ent.gz | 127.1 KB | Display | PDB format |
PDBx/mmJSON format | 6os6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/os/6os6 ftp://data.pdbj.org/pub/pdb/validation_reports/os/6os6 | HTTPS FTP |
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-Related structure data
Related structure data | 6os3C 6os5C 5jxmS 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 41064.328 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salinispora arenicola (strain CNS-205) (bacteria) Strain: CNS-205 / Gene: Sare_4565 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A8M6W6 |
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-Non-polymers , 6 types, 417 molecules
#2: Chemical | ChemComp-DST / | ||||||
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#3: Chemical | ChemComp-TRP / | ||||||
#4: Chemical | #5: Chemical | ChemComp-CL / | #6: Chemical | ChemComp-BEZ / | #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.62 Å3/Da / Density % sol: 53.13 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop Details: 1% (w/v) tryptone, 0.05 M HEPES-Na (pH 7.0), 12% PEG 3350 PH range: 7.0 - 7.4 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.97932 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 1, 2019 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97932 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.33→29.12 Å / Num. obs: 95021 / % possible obs: 99.8 % / Redundancy: 7.5 % / Biso Wilson estimate: 13.86 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.027 / Rrim(I) all: 0.075 / Net I/σ(I): 15 / Num. measured all: 708407 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Author used SWISS-MODEL server to generate a phasing model based on the protein sequence. SWISS-MODEL produced a phasing model based on PDB Entry 5JXM. Author used the polyALA version ...Starting model: Author used SWISS-MODEL server to generate a phasing model based on the protein sequence. SWISS-MODEL produced a phasing model based on PDB Entry 5JXM. Author used the polyALA version of the model for phasing. Resolution: 1.33→29.118 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 16.8
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 65.86 Å2 / Biso mean: 18.9029 Å2 / Biso min: 8.35 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.33→29.118 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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