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Yorodumi- PDB-5itv: Crystal structure of Bacillus subtilis BacC Dihydroanticapsin 7-d... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5itv | ||||||
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Title | Crystal structure of Bacillus subtilis BacC Dihydroanticapsin 7-dehydrogenase in complex with NADH | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.26 Å | ||||||
Authors | Perinbam, K. / Balaram, H. / Row, T.N.G. / Gopal, B. | ||||||
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 | 5itv.cif.gz | 197.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5itv.ent.gz | 158.9 KB | Display | PDB format |
PDBx/mmJSON format | 5itv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/it/5itv ftp://data.pdbj.org/pub/pdb/validation_reports/it/5itv | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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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 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-NAI / #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: 2.3 Å3/Da / Density % sol: 46.51 % |
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Crystal grow | Temperature: 291.15 K / Method: microbatch / pH: 6.5 Details: 0.2M Ammonium sulfate, 0.1M BIS-TRIS, pH 6.5, 25% w/v Polyethylene glycol 3350, 10% v/v Glycerol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Oct 15, 2014 |
Radiation | Monochromator: VariMax HF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.26→38.1 Å / Num. obs: 46073 / % possible obs: 99.8 % / Redundancy: 3.9 % / Biso Wilson estimate: 16.3 Å2 / CC1/2: 0.996 / Rsym value: 0.08 / Net I/σ(I): 12.9 |
Reflection shell | Resolution: 2.26→2.38 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.325 / Mean I/σ(I) obs: 3.8 / % possible all: 98.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.26→38.1 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.925 / SU B: 6.622 / SU ML: 0.16 / Cross valid method: THROUGHOUT / ESU R: 0.366 / ESU R Free: 0.213
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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: 25.385 Å2
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Refinement step | Cycle: 1 / Resolution: 2.26→38.1 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05
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LS refinement shell | Resolution: 2.256→2.315 Å / Total num. of bins used: 20
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