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Yorodumi- PDB-3ryk: 1.63 Angstrom resolution crystal structure of dTDP-4-dehydrorhamn... -
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-Basic information
Entry | Database: PDB / ID: 3ryk | |||||||||
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Title | 1.63 Angstrom resolution crystal structure of dTDP-4-dehydrorhamnose 3,5-epimerase (rfbC) from Bacillus anthracis str. Ames with TDP and PPi bound | |||||||||
Components | dTDP-4-dehydrorhamnose 3,5-epimerase | |||||||||
Keywords | ISOMERASE / dTDP-4-dehydrorhamnose 3 / 5-epimerase / rhamnose pathway / structural genomics / infectious diseases / Center for Structural Genomics of Infectious Diseases (CSGID) / jelly roll-like topology / The enzyme epimerizes at two carbon centers / the 3 and 5 positions of the sugar ring | |||||||||
Function / homology | Function and homology information dTDP-4-dehydrorhamnose 3,5-epimerase / dTDP-4-dehydrorhamnose 3,5-epimerase activity / O antigen biosynthetic process / dTDP-rhamnose biosynthetic process Similarity search - Function | |||||||||
Biological species | Bacillus anthracis str. Ames (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.631 Å | |||||||||
Authors | Halavaty, A.S. / Kuhn, M. / Minasov, G. / Shuvalova, L. / Kwon, K. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | |||||||||
Citation | Journal: Acta Crystallogr F Struct Biol Commun / Year: 2017 Title: Structure of the Bacillus anthracis dTDP-L-rhamnose-biosynthetic enzyme dTDP-4-dehydrorhamnose 3,5-epimerase (RfbC). Authors: Shornikov, A. / Tran, H. / Macias, J. / 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 | 3ryk.cif.gz | 169.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ryk.ent.gz | 132.4 KB | Display | PDB format |
PDBx/mmJSON format | 3ryk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ry/3ryk ftp://data.pdbj.org/pub/pdb/validation_reports/ry/3ryk | HTTPS FTP |
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-Related structure data
Related structure data | 1dzrS S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 23451.492 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus anthracis str. Ames (bacteria) Strain: Bacillus anthracis str. Ames / Gene: BAS1136, BA_1229, GBAA_1229, rfbC / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21/Magic References: UniProt: Q81TP1, UniProt: A0A6L7H6N0*PLUS, dTDP-4-dehydrorhamnose 3,5-epimerase #2: Chemical | ChemComp-POP / | #3: Chemical | ChemComp-TYD / | #4: 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: 2.08 Å3/Da / Density % sol: 40.99 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5 Details: Protein: 7.5 mg/mL in 10 mM Tris/HCl pH 8.3, 0.5 M NaCl, 5 mM BME. Crystallization condition: The JCSG+ suite (condition A3(#3): 0.2 M di-Ammonium citrate pH 5.0, 20 % w/v PEG3350). ...Details: Protein: 7.5 mg/mL in 10 mM Tris/HCl pH 8.3, 0.5 M NaCl, 5 mM BME. Crystallization condition: The JCSG+ suite (condition A3(#3): 0.2 M di-Ammonium citrate pH 5.0, 20 % w/v PEG3350). Crystallized at 1:1 v/v ratio. Cryo: soak in The JCSG+ A3. , VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97919 Å | |||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 17, 2011 / Details: Mirror | |||||||||||||||||||||||||
Radiation | Monochromator: Si(111) Channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97919 Å / Relative weight: 1 | |||||||||||||||||||||||||
Reflection twin |
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Reflection | Resolution: 1.63→30 Å / Num. all: 47039 / Num. obs: 47039 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Biso Wilson estimate: 24.6 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 26.53 | |||||||||||||||||||||||||
Reflection shell | Resolution: 1.63→1.66 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.488 / Mean I/σ(I) obs: 2.87 / Num. unique all: 2273 / % possible all: 98.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1DZR Resolution: 1.631→28.85 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.972 / SU B: 5.946 / SU ML: 0.073 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / ESU R Free: 0.015 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.231 Å2
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Refinement step | Cycle: LAST / Resolution: 1.631→28.85 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.631→1.674 Å / Total num. of bins used: 20
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