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- PDB-4hn0: Crystal Structure of ChmJ, a 3'-monoepimerase apoenzyme from Stre... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4hn0 | ||||||
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Title | Crystal Structure of ChmJ, a 3'-monoepimerase apoenzyme from Streptomyces bikiniensis | ||||||
![]() | Putative 3-epimerase in D-allose pathway | ||||||
![]() | UNKNOWN FUNCTION / 3'-monoepimerase / natural product / deoxysugar / chalcomycin / dTDP-mycinose / 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 | ![]() | 167.6 KB | Display | ![]() |
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PDB format | ![]() | 134.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 468.5 KB | Display | ![]() |
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Full document | ![]() | 481.9 KB | Display | |
Data in XML | ![]() | 33.1 KB | Display | |
Data in CIF | ![]() | 45.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4hmzSC ![]() 4hn1C S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 21949.441 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-EDO / #3: Chemical | ChemComp-CL / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.3 Å3/Da / Density % sol: 62.71 % |
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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: ADSC QUANTUM 210r / Detector: CCD / Date: Aug 4, 2012 |
Radiation | Monochromator: double crystal monochromator Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→100.12 Å / Num. obs: 53594 / % possible obs: 96 % / Redundancy: 6.7 % |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 1.74 / Num. unique all: 9437 / Rsym value: 0.43 / % possible all: 89.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 4HMZ Resolution: 2.2→30 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.935 / SU B: 5.953 / SU ML: 0.153 / Cross valid method: THROUGHOUT / ESU R: 0.234 / ESU R Free: 0.203 / 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: 47.672 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.257 Å / Total num. of bins used: 20
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