+Open data
-Basic information
Entry | Database: PDB / ID: 6b5e | ||||||
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Title | Mycobacterium tuberculosis RmlA in complex with dTDP-glucose | ||||||
Components | Glucose-1-phosphate thymidylyltransferase | ||||||
Keywords | TRANSFERASE / nucleotidyltransferase / product / sugar-modifying | ||||||
Function / homology | Function and homology information dTTP metabolic process / glucose-1-phosphate thymidylyltransferase / glucose-1-phosphate thymidylyltransferase activity / dTDP-rhamnose biosynthetic process / extracellular polysaccharide biosynthetic process / peptidoglycan-based cell wall / glucose metabolic process / magnesium ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | Brown, H.A. / Holden, H.M. | ||||||
Funding support | United States, 1items
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Citation | Journal: Protein Sci. / Year: 2018 Title: The structure of glucose-1-phosphate thymidylyltransferase from Mycobacterium tuberculosis reveals the location of an essential magnesium ion in the RmlA-type enzymes. Authors: Brown, H.A. / Thoden, J.B. / Tipton, P.A. / Holden, H.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6b5e.cif.gz | 490.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6b5e.ent.gz | 399.8 KB | Display | PDB format |
PDBx/mmJSON format | 6b5e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b5/6b5e ftp://data.pdbj.org/pub/pdb/validation_reports/b5/6b5e | HTTPS FTP |
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-Related structure data
Related structure data | 6b5kSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-Protein , 1 types, 8 molecules ABCDEFGH
#1: Protein | Mass: 32592.039 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria) Strain: ATCC 25618 / H37Rv / Gene: rmlA, rfbA, Rv0334 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P9WH13, glucose-1-phosphate thymidylyltransferase |
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-Non-polymers , 7 types, 1506 molecules
#2: Chemical | ChemComp-DAU / #3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-TYD / #5: Chemical | ChemComp-CL / | #6: Chemical | ChemComp-EDO / | #7: Chemical | #8: 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: 2.34 Å3/Da / Density % sol: 47.49 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9 Details: 20% poly(ethylene glycol) 3350, 200 mM KCl, 100 mM CHES |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9794 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 24, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→50 Å / Num. obs: 195396 / % possible obs: 97.7 % / Redundancy: 6.5 % / Rsym value: 0.103 / Net I/σ(I): 45.8 |
Reflection shell | Resolution: 1.85→1.92 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 14.9 / Num. unique obs: 18536 / Rsym value: 0.179 / % possible all: 93.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6B5K Resolution: 1.85→50 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.934 / SU B: 2.732 / SU ML: 0.084 / Cross valid method: THROUGHOUT / ESU R: 0.139 / ESU R Free: 0.134 / 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: 26.419 Å2
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Refinement step | Cycle: 1 / Resolution: 1.85→50 Å
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Refine LS restraints |
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