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Yorodumi- PDB-1wlt: Crystal Structure of dTDP-4-dehydrorhamnose 3,5-epimerase homolog... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1wlt | ||||||
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Title | Crystal Structure of dTDP-4-dehydrorhamnose 3,5-epimerase homologue from Sulfolobus tokodaii | ||||||
Components | 176aa long hypothetical dTDP-4-dehydrorhamnose 3,5-epimerase | ||||||
Keywords | ISOMERASE / jelly roll-like topology / flattened barrel | ||||||
Function / homology | Function and homology information dTDP-4-dehydrorhamnose 3,5-epimerase / dTDP-4-dehydrorhamnose 3,5-epimerase activity / dTDP-rhamnose biosynthetic process / extracellular polysaccharide biosynthetic process / cytosol Similarity search - Function | ||||||
Biological species | Sulfolobus tokodaii (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Watanabe, N. / Sakai, N. / Zilian, Z. / Kawarabayasi, Y. / Tanaka, I. | ||||||
Citation | Journal: to be published Title: Crystal Structure of dTDP-4-dehydrorhamnose 3,5-epimerase homologue Authors: Watanabe, N. / Sakai, N. / Zilian, Z. / Kawarabayasi, Y. / Tanaka, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1wlt.cif.gz | 91.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1wlt.ent.gz | 69.1 KB | Display | PDB format |
PDBx/mmJSON format | 1wlt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1wlt_validation.pdf.gz | 443 KB | Display | wwPDB validaton report |
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Full document | 1wlt_full_validation.pdf.gz | 447.2 KB | Display | |
Data in XML | 1wlt_validation.xml.gz | 18.1 KB | Display | |
Data in CIF | 1wlt_validation.cif.gz | 26.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wl/1wlt ftp://data.pdbj.org/pub/pdb/validation_reports/wl/1wlt | 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 in the asymmetric unit. |
-Components
#1: Protein | Mass: 22677.107 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfolobus tokodaii (archaea) / Plasmid: pET23q / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) References: UniProt: Q96Z62, dTDP-4-dehydrorhamnose 3,5-epimerase #2: 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: 2.5 Å3/Da / Density % sol: 49.4 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 15% PEG 3350, 0.1M Sodium cacodylate buffer, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 2, 2004 / Details: MONOCHROMETER |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.89→50 Å / Num. all: 35811 / Num. obs: 35811 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 6.6 % / Biso Wilson estimate: 24.5 Å2 / Rsym value: 0.06 / Net I/σ(I): 15.5 |
Reflection shell | Resolution: 1.89→1.96 Å / Redundancy: 6.3 % / Mean I/σ(I) obs: 6.43 / Num. unique all: 3486 / Rsym value: 0.379 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1DZR Resolution: 1.9→20 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.927 / SU B: 3.349 / SU ML: 0.1 / Cross valid method: THROUGHOUT / ESU R: 0.15 / ESU R Free: 0.147 / 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: 26.019 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 Å / Total num. of bins used: 20
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