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Yorodumi- PDB-6bi4: 2.9 Angstrom Resolution Crystal Structure of dTDP-Glucose 4,6-deh... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6bi4 | ||||||||||||
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Title | 2.9 Angstrom Resolution Crystal Structure of dTDP-Glucose 4,6-dehydratase (rfbB) from Bacillus anthracis str. Ames in Complex with NAD. | ||||||||||||
Components | dTDP-glucose 4,6-dehydratase | ||||||||||||
Keywords | LYASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / dTDP-Glucose 4 / 6-dehydratase / NAD | ||||||||||||
Function / homology | Function and homology information dTDP-glucose 4,6-dehydratase / dTDP-glucose 4,6-dehydratase activity / nucleotide-sugar metabolic process Similarity search - Function | ||||||||||||
Biological species | Bacillus anthracis str. Ames (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.91 Å | ||||||||||||
Authors | Halavaty, A.S. / Kuhn, M. / Shuvalova, L. / Minasov, G. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||||||||
Citation | Journal: J.Struct.Biol. / Year: 2018 Title: Structure of the Bacillus anthracis dTDP-l-rhamnose biosynthetic pathway enzyme: dTDP-alpha-d-glucose 4,6-dehydratase, RfbB. Authors: Gokey, T. / Halavaty, A.S. / Minasov, G. / Anderson, W.F. / Kuhn, M.L. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6bi4.cif.gz | 527.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6bi4.ent.gz | 437 KB | Display | PDB format |
PDBx/mmJSON format | 6bi4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bi/6bi4 ftp://data.pdbj.org/pub/pdb/validation_reports/bi/6bi4 | HTTPS FTP |
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-Related structure data
Related structure data | 1r66S S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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2 |
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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: ALA / Beg label comp-ID: ALA / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: 0 / Auth seq-ID: 0 - 321 / Label seq-ID: 24 - 345
NCS ensembles :
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-Components
-Protein / Sugars , 2 types, 6 molecules ABCD
#1: Protein | Mass: 39928.996 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus anthracis str. Ames (bacteria) Strain: Ames / Gene: rfbB / Plasmid: pMCSG19c / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)Magic References: UniProt: Q81TP0, UniProt: A0A6L7HMN5*PLUS, dTDP-glucose 4,6-dehydratase #2: Polysaccharide | |
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-Non-polymers , 4 types, 96 molecules
#3: Chemical | #4: Chemical | ChemComp-NAD / #5: Chemical | ChemComp-SO4 / #6: 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: 3.14 Å3/Da / Density % sol: 60.8 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8 Details: PROTEIN: TOTAL RFBB AND RFBC AT 7.5 MG/ML IN 10 MM TRIS HCL PH 8.3, 500 MM NACL, 5 MM BME, 10% GLYCEROL, 5 MM MGCL2, AND 1 MM NAD+. SCREEN: 0.1 M TRIS HCL PH 8.0, 1.56 M AMMONIUM SULFATE, ...Details: PROTEIN: TOTAL RFBB AND RFBC AT 7.5 MG/ML IN 10 MM TRIS HCL PH 8.3, 500 MM NACL, 5 MM BME, 10% GLYCEROL, 5 MM MGCL2, AND 1 MM NAD+. SCREEN: 0.1 M TRIS HCL PH 8.0, 1.56 M AMMONIUM SULFATE, AND 8.5% (W/V) PEG3350. CRYO-PROTECTANT SOLUTION: 1:1 RATIO OF 3.6 M AMMONIUM SULFATE AND 50% SUCROSE. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 20, 2012 / Details: C(111) |
Radiation | Monochromator: Be / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97856 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→30 Å / Num. obs: 44858 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 9.4 % / Biso Wilson estimate: 69.2 Å2 / Rmerge(I) obs: 0.15 / Rpim(I) all: 0.051 / Rrim(I) all: 0.158 / Rsym value: 0.15 / Χ2: 1.004 / Net I/σ(I): 13 |
Reflection shell | Resolution: 2.9→2.95 Å / Redundancy: 9.7 % / Rmerge(I) obs: 0.771 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 2208 / CC1/2: 0.843 / Rpim(I) all: 0.256 / Rrim(I) all: 0.813 / Rsym value: 0.771 / Χ2: 1.002 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1R66 Resolution: 2.91→29.95 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.938 / SU B: 25.627 / SU ML: 0.229 / Cross valid method: THROUGHOUT / ESU R: 1.626 / ESU R Free: 0.299 / 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: 66.28 Å2
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Refinement step | Cycle: 1 / Resolution: 2.91→29.95 Å
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