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Yorodumi- PDB-6zrx: Crystal structure of 6-dimethylallyltryptophan synthase from Micr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6zrx | ||||||
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Title | Crystal structure of 6-dimethylallyltryptophan synthase from Micromonospora olivasterospora in complex with DMASPP and Trp | ||||||
Components | DMATS type aromatic prenyltransferase | ||||||
Keywords | TRANSFERASE / Complex / ABBA-barrel fold / Prenyltransferase | ||||||
Function / homology | Aromatic prenyltransferase, DMATS-type / Tryptophan dimethylallyltransferase / Aromatic prenyltransferase / transferase activity, transferring alkyl or aryl (other than methyl) groups / alkaloid metabolic process / Chem-6C7 / DI(HYDROXYETHYL)ETHER / TRYPTOPHAN / DMATS type aromatic prenyltransferase Function and homology information | ||||||
Biological species | Micromonospora olivasterospora (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Ostertag, E. / Stehle, T. / Zocher, G. | ||||||
Funding support | Germany, 1items
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Citation | Journal: J.Mol.Biol. / Year: 2020 Title: Reprogramming Substrate and Catalytic Promiscuity of Tryptophan Prenyltransferases. Authors: Ostertag, E. / Zheng, L. / Broger, K. / Stehle, T. / Li, S.M. / Zocher, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6zrx.cif.gz | 314.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6zrx.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6zrx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6zrx_validation.pdf.gz | 2.7 MB | Display | wwPDB validaton report |
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Full document | 6zrx_full_validation.pdf.gz | 2.7 MB | Display | |
Data in XML | 6zrx_validation.xml.gz | 60.9 KB | Display | |
Data in CIF | 6zrx_validation.cif.gz | 88.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zr/6zrx ftp://data.pdbj.org/pub/pdb/validation_reports/zr/6zrx | HTTPS FTP |
-Related structure data
Related structure data | 6zryC 6zrzC 6zs0C 5injS 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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2 |
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3 |
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4 |
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Unit cell |
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-Components
-Protein , 1 types, 4 molecules AAABBBCCCDDD
#1: Protein | Mass: 39210.191 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Micromonospora olivasterospora (bacteria) Gene: MolI14.36, JD77_02062 / Production host: Escherichia coli (E. coli) / References: UniProt: Q2MFY2 |
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-Non-polymers , 5 types, 988 molecules
#2: Chemical | ChemComp-6C7 / #3: Chemical | ChemComp-TRP / #4: Chemical | ChemComp-PEG / #5: Chemical | ChemComp-NA / | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 2.11 Å3/Da / Density % sol: 41.81 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / Details: 200 mM Calcium acetate, 26% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.00001 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 6, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00001 Å / Relative weight: 1 |
Reflection | Resolution: 1.69→39.673 Å / Num. obs: 143483 / % possible obs: 98.5 % / Redundancy: 4 % / Biso Wilson estimate: 30.3 Å2 / CC1/2: 0.99 / Rrim(I) all: 0.09 / Net I/σ(I): 11.3 |
Reflection shell | Resolution: 1.69→1.79 Å / Redundancy: 4 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 92053 / CC1/2: 0.82 / Rrim(I) all: 0.68 / % possible all: 98.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5INJ Resolution: 1.7→39.673 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.946 / WRfactor Rfree: 0.239 / WRfactor Rwork: 0.204 / SU B: 2.863 / SU ML: 0.093 / Average fsc free: 0.9051 / Average fsc work: 0.9139 / Cross valid method: FREE R-VALUE / ESU R: 0.129 / ESU R Free: 0.118 Details: Hydrogens have been added in their 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 / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.708 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→39.673 Å
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Refine LS restraints |
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LS refinement shell |
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