+Open data
-Basic information
Entry | Database: PDB / ID: 7s3t | |||||||||
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Title | NzeB Diketopiperazine Dimerase Mutant: Q68I-G87A-A89G-I90V | |||||||||
Components | NascB | |||||||||
Keywords | BIOSYNTHETIC PROTEIN / Cytochrome P450 / Diketopiperazine dimerase / Natural Products | |||||||||
Function / homology | Function and homology information oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / monooxygenase activity / iron ion binding / heme binding Similarity search - Function | |||||||||
Biological species | Streptomyces sp. (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | |||||||||
Authors | Harris, N.R. / Shende, V.V. / Sanders, J.N. / Newmister, S.A. / Khatri, Y. / Movassaghi, M. / Houk, K.N. / Sherman, D.H. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2023 Title: Molecular Dynamics Simulations Guide Chimeragenesis and Engineered Control of Chemoselectivity in Diketopiperazine Dimerases. Authors: Shende, V.V. / Harris, N.R. / Sanders, J.N. / Newmister, S.A. / Khatri, Y. / Movassaghi, M. / Houk, K.N. / Sherman, D.H. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7s3t.cif.gz | 106.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7s3t.ent.gz | 76.5 KB | Display | PDB format |
PDBx/mmJSON format | 7s3t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s3/7s3t ftp://data.pdbj.org/pub/pdb/validation_reports/s3/7s3t | HTTPS FTP |
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-Related structure data
Related structure data | 7s3jC 6xaiS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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: 43833.504 Da / Num. of mol.: 1 / Mutation: Q68I,G87A,A89G,I90V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces sp. (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A3G1Q973 |
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-Non-polymers , 5 types, 373 molecules
#2: Chemical | ChemComp-HEM / | ||||||
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#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-MG / | #6: Water | ChemComp-HOH / | |
-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: 2.32 Å3/Da / Density % sol: 46.87 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 2M Magnesium Chloride 0.1M Tris HCl pH 8.5 26% PEG 3350 4% ethylene glycol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 10, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.033 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→45.48 Å / Num. obs: 462696 / % possible obs: 93.8 % / Redundancy: 6.3 % / Biso Wilson estimate: 16.64 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.05348 / Rpim(I) all: 0.02244 / Rrim(I) all: 0.05812 / Net I/σ(I): 17.9 |
Reflection shell | Resolution: 1.4→1.45 Å / Rmerge(I) obs: 0.4283 / Mean I/σ(I) obs: 2.62 / Num. unique obs: 20759 / CC1/2: 0.898 / CC star: 0.973 / Rpim(I) all: 0.2343 / Rrim(I) all: 0.4905 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6XAI Resolution: 1.4→45.48 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 21.77 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 68.43 Å2 / Biso mean: 22.4086 Å2 / Biso min: 6.76 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.4→45.48 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 28
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