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Yorodumi- PDB-5ump: Crystal structure of TnmS3, an antibiotic binding protein from St... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ump | ||||||
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Title | Crystal structure of TnmS3, 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-2 / Protein Structure Initiative / 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: 1.08 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 | 5ump.cif.gz | 70.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ump.ent.gz | 49.7 KB | Display | PDB format |
PDBx/mmJSON format | 5ump.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/um/5ump ftp://data.pdbj.org/pub/pdb/validation_reports/um/5ump | HTTPS FTP |
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-Related structure data
Related structure data | 5umqC 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: 15152.925 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces sp. CB03234 (bacteria) / Gene: tnmS3 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A125SA29 #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: 2.14 Å3/Da / Density % sol: 42.55 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 100 mM ammonium acetate, 100 mM bis-tris, and 17% w/v polyethylene glycol 3350 |
-Data collection
Diffraction | Mean temperature: 77 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 4, 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: 1.08→40 Å / Num. obs: 106971 / % possible obs: 95.3 % / Redundancy: 6.4 % / CC1/2: 0.997 / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.021 / Rrim(I) all: 0.054 / Net I/σ(I): 31.6 |
Reflection shell | Resolution: 1.08→1.1 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 1.9 / Num. unique all: 4861 / Num. unique obs: 4861 / CC1/2: 0.794 / Rpim(I) all: 0.298 / Rrim(I) all: 0.691 / % possible all: 88 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4HC5 Resolution: 1.08→40 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.961 / SU B: 0.454 / SU ML: 0.023 / Cross valid method: THROUGHOUT / ESU R: 0.032 / ESU R Free: 0.034 / 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: 15.641 Å2
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Refinement step | Cycle: 1 / Resolution: 1.08→40 Å
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Refine LS restraints |
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