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Yorodumi- PDB-5umq: Crystal structure of TnmS1, an antibiotic binding protein from St... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5umq | ||||||
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Title | Crystal structure of TnmS1, an antibiotic binding protein from Streptomyces sp. CB03234 | ||||||
Components | Glyoxalase/bleomycin resisance protein/dioxygenase | ||||||
Keywords | Tiancimycin-binding protein / glyoxalase/bleomycin resistance protein/dioxygenase superfamily / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / Enzyme Discovery for Natural Product Biosynthesis / NatPro | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Streptomyces sp. CB03234 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Chang, C.Y. / Chang, C. / Nocek, B. / Rudolf, J.D. / Joachimiak, A. / Phillips Jr., G.N. / Shen, B. / Enzyme Discovery for Natural Product Biosynthesis (NatPro) / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: Cell Chem Biol / Year: 2018 Title: Resistance to Enediyne Antitumor Antibiotics by Sequestration. Authors: Chang, C.Y. / Yan, X. / Crnovcic, I. / Annaval, T. / Chang, C. / Nocek, B. / Rudolf, J.D. / Yang, D. / Babnigg, G. / Joachimiak, A. / Phillips Jr., G.N. / Shen, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5umq.cif.gz | 67.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5umq.ent.gz | 48 KB | Display | PDB format |
PDBx/mmJSON format | 5umq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/um/5umq ftp://data.pdbj.org/pub/pdb/validation_reports/um/5umq | HTTPS FTP |
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-Related structure data
Related structure data | 5umpC 5umwC 5umxC 5umyC 6bbxC 4hc5S 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
#1: Protein | Mass: 16068.983 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces sp. CB03234 (bacteria) / Gene: tnmS1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A125SA24 #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: 1.94 Å3/Da / Density % sol: 36.73 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 50 mM ammonium sulphate, 50 mM bis-tris propane, and 30 % v/v pentaerythriol ethoxylate (15/4 EO/OH) |
-Data collection
Diffraction | Mean temperature: 80 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97934 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 7, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97934 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→50 Å / Num. obs: 18652 / % possible obs: 98.4 % / Redundancy: 13.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.02 / Rrim(I) all: 0.074 / Net I/σ(I): 33 |
Reflection shell | Resolution: 1.95→1.98 Å / Redundancy: 9.6 % / Rmerge(I) obs: 0.761 / Mean I/σ(I) obs: 2.4 / Num. unique all: 890 / Num. unique obs: 890 / CC1/2: 0.88 / Rpim(I) all: 0.242 / Rrim(I) all: 0.802 / % possible all: 97.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4HC5 Resolution: 1.95→50 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.891 / SU B: 3.787 / SU ML: 0.11 / Cross valid method: THROUGHOUT / ESU R: 0.206 / ESU R Free: 0.188 / 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: 23.311 Å2
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Refinement step | Cycle: 1 / Resolution: 1.95→50 Å
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Refine LS restraints |
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