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Yorodumi- PDB-8rz6: SeMet derivative structure of the condensation domain TomBC from ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8rz6 | ||||||
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Title | SeMet derivative structure of the condensation domain TomBC from the Tomaymycin non-ribosomal peptide synthetase | ||||||
Components | Tomaymycin non-ribosomal peptide synthetase | ||||||
Keywords | BIOSYNTHETIC PROTEIN / Non-ribosomal peptide synthetase / Tomaymycin / Condensation | ||||||
Function / homology | FORMIC ACID / : Function and homology information | ||||||
Biological species | Streptomyces regensis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å | ||||||
Authors | Karanth, M. / Schmelz, S. / Kirkpatrick, J. / Krausze, J. / Scrima, A. / Carlomagno, T. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Sci Adv / Year: 2024 Title: The specificity of intermodular recognition in a prototypical nonribosomal peptide synthetase depends on an adaptor domain. Authors: Karanth, M.N. / Kirkpatrick, J.P. / Krausze, J. / Schmelz, S. / Scrima, A. / Carlomagno, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8rz6.cif.gz | 348.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8rz6.ent.gz | 285.5 KB | Display | PDB format |
PDBx/mmJSON format | 8rz6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8rz6_validation.pdf.gz | 459 KB | Display | wwPDB validaton report |
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Full document | 8rz6_full_validation.pdf.gz | 465.4 KB | Display | |
Data in XML | 8rz6_validation.xml.gz | 38.2 KB | Display | |
Data in CIF | 8rz6_validation.cif.gz | 57 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rz/8rz6 ftp://data.pdbj.org/pub/pdb/validation_reports/rz/8rz6 | HTTPS FTP |
-Related structure data
Related structure data | 8qnfC 8qpyC 8qrxC 8qsxC 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
#1: Protein | Mass: 59713.070 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: SeMet derivative structure of the condensation domain TomBC from Tomaymycin non-ribosomal peptide synthetase Source: (gene. exp.) Streptomyces regensis (bacteria) / Variant: FH6421 / Production host: Escherichia coli (E. coli) #2: Chemical | ChemComp-FMT / #3: Chemical | ChemComp-K / #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | N | Has protein modification | 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: 3.43 Å3/Da / Density % sol: 64.11 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 100 mM Tris pH 8.5, 3.0 M KFormate, with 25% glycerol used as cryoprotectant |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.979733 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 7, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979733 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→48.91 Å / Num. obs: 139112 / % possible obs: 99.1 % / Redundancy: 10.58 % / CC1/2: 0.994 / Net I/σ(I): 9.9 |
Reflection shell | Resolution: 2.3→2.4 Å / Redundancy: 10.82 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 16569 / CC1/2: 0.747 / % possible all: 98.7 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.3→48.91 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 21.75 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→48.91 Å
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Refine LS restraints |
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LS refinement shell |
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