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- PDB-4hmz: Crystal Structure of ChmJ, a 3'-monoepimerase from Streptomyces b... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4hmz | ||||||
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Title | Crystal Structure of ChmJ, a 3'-monoepimerase from Streptomyces bikiniensis in complex with dTDP-quinovose | ||||||
![]() | Putative 3-epimerase in D-allose pathway | ||||||
![]() | UNKNOWN FUNCTION / 3'-monoepimerase / natural product / deoxysugar / chalcomycin / dTDP-mycinose / dTDP-quinovose / Cupin fold / nucleotide-linked sugar / Epimerization | ||||||
Function / homology | ![]() dTDP-4-dehydro-6-deoxy-D-glucose 3-epimerase / dTDP-4-dehydrorhamnose 3,5-epimerase activity / dTDP-rhamnose biosynthetic process / extracellular polysaccharide biosynthetic process / antibiotic biosynthetic process / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Holden, H.M. / Kubiak, R.L. | ||||||
![]() | ![]() Title: Structural and Functional Studies on a 3'-Epimerase Involved in the Biosynthesis of dTDP-6-deoxy-d-allose. Authors: Kubiak, R.L. / Phillips, R.K. / Zmudka, M.W. / Ahn, M.R. / Maka, E.M. / Pyeatt, G.L. / Roggensack, S.J. / Holden, H.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 177.2 KB | Display | ![]() |
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PDB format | ![]() | 143.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 474.2 KB | Display | ![]() |
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Full document | ![]() | 483.1 KB | Display | |
Data in XML | ![]() | 32.9 KB | Display | |
Data in CIF | ![]() | 47.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4hn0C ![]() 4hn1C ![]() 2c0zS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 22225.734 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-EDO / #3: Sugar | ChemComp-18T / [( #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.28 Å3/Da / Density % sol: 62.48 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 20% PEG 3400, 2% 2-methyl-2,4-pentanediol, 100 mM MOPS, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: Bruker Platinum 135 / Detector: CCD / Date: Apr 10, 2012 / Details: Montel |
Radiation | Monochromator: Nickel filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→99.5 Å / Num. all: 77282 / Num. obs: 73347 / % possible obs: 94.9 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.088 |
Reflection shell | Resolution: 2→2.1 Å / Redundancy: 1.78 % / Mean I/σ(I) obs: 1.95 / Num. unique all: 9355 / Rsym value: 0.31 / % possible all: 89.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 2C0Z Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.913 / SU B: 4.194 / SU ML: 0.115 / Cross valid method: THROUGHOUT / ESU R: 0.166 / ESU R Free: 0.162 / 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: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.47 Å2
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Refinement step | Cycle: LAST / Resolution: 2→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20
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