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Yorodumi- PDB-5itw: Crystal structure of Bacillus subtilis BacC Dihydroanticapsin 7-d... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5itw | |||||||||
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Title | Crystal structure of Bacillus subtilis BacC Dihydroanticapsin 7-dehydrogenase | |||||||||
Components | Dihydroanticapsin 7-dehydrogenase | |||||||||
Keywords | OXIDOREDUCTASE / short-chain dehydrogenases/reductases / Rossmann fold / NAD(P) binding domain | |||||||||
Function / homology | Function and homology information dihydroanticapsin dehydrogenase / antibiotic biosynthetic process / oxidoreductase activity Similarity search - Function | |||||||||
Biological species | Bacillus subtilis (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.19 Å | |||||||||
Authors | Perinbam, K. / Balaram, H. / Row, T.N.G. / Gopal, B. | |||||||||
Funding support | India, 2items
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Citation | Journal: Protein Eng. Des. Sel. / Year: 2017 Title: Probing the influence of non-covalent contact networks identified by charge density analysis on the oxidoreductase BacC. Authors: Perinbam, K. / Balaram, H. / Guru Row, T.N. / Gopal, B. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5itw.cif.gz | 410.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5itw.ent.gz | 336.8 KB | Display | PDB format |
PDBx/mmJSON format | 5itw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/it/5itw ftp://data.pdbj.org/pub/pdb/validation_reports/it/5itw | HTTPS FTP |
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-Related structure data
Related structure data | 5itvC 3awdS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: GLN / End label comp-ID: GLN / Refine code: 0 / Auth seq-ID: 1 - 255 / Label seq-ID: 1 - 255
NCS ensembles :
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-Components
#1: Protein | Mass: 27350.293 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: sulfate ions are modelled Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria) Strain: 168 / Gene: bacC, ywfD, BSU37720, ipa-82d / Plasmid: pET22b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: P39640, dihydroanticapsin dehydrogenase #2: Chemical | ChemComp-SO4 / #3: 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: 2.25 Å3/Da / Density % sol: 45.4 % |
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Crystal grow | Temperature: 291.15 K / Method: microbatch / pH: 6.5 Details: 0.2M Ammonium sulfate, 0.1M BIS-TRIS pH6.5, 25% w/v Polyethylene glycol 3350, 10% glycerol cryoprotectant, 0.05M Tris, 0.25M NaCl |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.95372 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 12, 2014 |
Radiation | Monochromator: Band pass 1.9x10-4 for a Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95372 Å / Relative weight: 1 |
Reflection | Resolution: 1.187→32.95 Å / Num. obs: 305981 / % possible obs: 99.6 % / Redundancy: 4.1 % / Biso Wilson estimate: 10.1 Å2 / CC1/2: 0.998 / Rsym value: 0.071 / Net I/σ(I): 9.2 |
Reflection shell | Resolution: 1.187→1.25 Å / Redundancy: 3.8 % / Rmerge(I) obs: 1.067 / Mean I/σ(I) obs: 1.5 / % possible all: 97.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3AWD Resolution: 1.19→32.95 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.974 / SU B: 1.581 / SU ML: 0.03 / Cross valid method: THROUGHOUT / ESU R: 0.034 / 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: 18.258 Å2
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Refinement step | Cycle: LAST / Resolution: 1.19→32.95 Å
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Refine LS restraints |
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