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Yorodumi- PDB-1rtv: RmlC (dTDP-6-deoxy-D-xylo-4-hexulose 3,5-epimerase) crystal struc... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1rtv | ||||||
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Title | RmlC (dTDP-6-deoxy-D-xylo-4-hexulose 3,5-epimerase) crystal structure from Pseudomonas aeruginosa, apo structure | ||||||
Components | dTDP-4-dehydrorhamnose 3,5-epimerase | ||||||
Keywords | ISOMERASE / RmlC / main beta sheet structure | ||||||
Function / homology | Function and homology information dTDP-4-dehydrorhamnose 3,5-epimerase / dTDP-4-dehydrorhamnose 3,5-epimerase activity / dTDP-rhamnose biosynthetic process / lipopolysaccharide core region biosynthetic process / lipopolysaccharide biosynthetic process / extracellular polysaccharide biosynthetic process / cytosol Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Dong, C.J. / Naismith, J.H. | ||||||
Citation | Journal: TO BE PUBLISHED Title: RmlC (dTDP-6-deoxy-D-xylo-4-hexulose 3,5-epimerase) crystal structure from Pseudomonas aeruginosa, apo structure Authors: Dong, C.J. / Naismith, J.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1rtv.cif.gz | 51.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1rtv.ent.gz | 36.1 KB | Display | PDB format |
PDBx/mmJSON format | 1rtv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1rtv_validation.pdf.gz | 441 KB | Display | wwPDB validaton report |
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Full document | 1rtv_full_validation.pdf.gz | 448.9 KB | Display | |
Data in XML | 1rtv_validation.xml.gz | 10.7 KB | Display | |
Data in CIF | 1rtv_validation.cif.gz | 13.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rt/1rtv ftp://data.pdbj.org/pub/pdb/validation_reports/rt/1rtv | HTTPS FTP |
-Related structure data
Related structure data | 1dzrS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The biological assembly is a dimer. |
-Components
#1: Protein | Mass: 21082.795 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: rmlc / Plasmid: pET23a(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: Q9HU21, dTDP-4-dehydrorhamnose 3,5-epimerase |
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#2: Chemical | ChemComp-SRT / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.2 Å3/Da / Density % sol: 61.6 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.2M Sodium tartrate, 0.1M MOPS, 8% PEG 8000, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ROTATING ANODE / Type: ENRAF-NONIUS / Wavelength: 1.5418 Å |
Detector | Type: MAC Science DIP-2000 / Detector: IMAGE PLATE / Date: May 10, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→40.4 Å / Num. all: 9732 / Num. obs: 9710 / % possible obs: 99.2 % / Observed criterion σ(F): 2.367 / Observed criterion σ(I): 1.8 / Redundancy: 7.3 % / Biso Wilson estimate: 56.26 Å2 / Rmerge(I) obs: 0.094 / Rsym value: 0.088 / Net I/σ(I): 6.8 |
Reflection shell | Resolution: 2.5→2.67 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.455 / Mean I/σ(I) obs: 4 / Num. unique all: 1298 / Rsym value: 0.419 / % possible all: 94.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1DZR Resolution: 2.5→54.23 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.87 / SU B: 14.086 / SU ML: 0.315 / Isotropic thermal model: overall / Cross valid method: THROUGHOUT / σ(F): 2.36 / σ(I): 1.8 / ESU R: 0.425 / ESU R Free: 0.307 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.642 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→54.23 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.565 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 4.482 Å / Origin y: 41.222 Å / Origin z: 28.744 Å
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