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Yorodumi- PDB-8ccm: Crystal structure of Mycobacterium smegmatis thioredoxin reductas... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8ccm | ||||||
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Title | Crystal structure of Mycobacterium smegmatis thioredoxin reductase in complex with Compound 2-06 | ||||||
Components | Thioredoxin reductase | ||||||
Keywords | OXIDOREDUCTASE / TrxR | ||||||
Function / homology | Function and homology information thioredoxin-disulfide reductase / thioredoxin-disulfide reductase (NADPH) activity / removal of superoxide radicals / cell redox homeostasis / cytosol Similarity search - Function | ||||||
Biological species | Mycolicibacterium smegmatis MC2 155 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 Å | ||||||
Authors | Fuesser, F.T. / Koch, O. / Kuemmel, D. | ||||||
Funding support | Germany, 1items
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Citation | Journal: To Be Published Title: Fragment-based design of mycobacterial thioredoxin reductase inhibitors based on computational exploration of a huge virtual space Authors: Fuesser, F.T. / Kuemmel, D. / Koch, O. / Otten, P. / Junker, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ccm.cif.gz | 167.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ccm.ent.gz | 108.2 KB | Display | PDB format |
PDBx/mmJSON format | 8ccm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8ccm_validation.pdf.gz | 976.3 KB | Display | wwPDB validaton report |
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Full document | 8ccm_full_validation.pdf.gz | 975.5 KB | Display | |
Data in XML | 8ccm_validation.xml.gz | 15.7 KB | Display | |
Data in CIF | 8ccm_validation.cif.gz | 22.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cc/8ccm ftp://data.pdbj.org/pub/pdb/validation_reports/cc/8ccm | HTTPS FTP |
-Related structure data
Related structure data | 8ccjC 8cckC 8cclC 8cciS 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 on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 34578.730 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycolicibacterium smegmatis MC2 155 (bacteria) Gene: trxB / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: I7FW12 |
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-Non-polymers , 7 types, 194 molecules
#2: Chemical | ChemComp-FAD / | ||||||||
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#3: Chemical | ChemComp-U9C / ~{ Mass: 256.326 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H12N4S / Feature type: SUBJECT OF INVESTIGATION | ||||||||
#4: Chemical | #5: Chemical | ChemComp-GOL / | #6: Chemical | #7: Chemical | #8: 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: 3 Å3/Da / Density % sol: 59.04 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.4 Details: Sodium malonate dibasic monohydrate 2.16 M, Glycerol 10%, pH7.4 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Apr 14, 2022 |
Radiation | Monochromator: Si111-DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 1.73→46.94 Å / Num. obs: 44354 / % possible obs: 99.78 % / Redundancy: 9.9 % / Biso Wilson estimate: 28.47 Å2 / CC1/2: 0.99 / Net I/σ(I): 8.81 |
Reflection shell | Resolution: 1.73→1.792 Å / Mean I/σ(I) obs: 0.54 / Num. unique obs: 4394 / CC1/2: 0.49 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 8CCI Resolution: 1.73→38.86 Å / SU ML: 0.2839 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.4281 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 42.33 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.73→38.86 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A
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