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- PDB-6d9d: Crystal structure of Corynebacterium diphtheriae UDP-galactopyran... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6d9d | ||||||||||||
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Title | Crystal structure of Corynebacterium diphtheriae UDP-galactopyranose mutase in complex with UDP-GlcNAc (open, oxidized) | ||||||||||||
![]() | UDP-galactopyranose mutase | ||||||||||||
![]() | ISOMERASE / galatofuranose / galactopyranose / galactose / UDP / enzyme / UDP-galactopyranose mutase | ||||||||||||
Function / homology | NAD(P)-binding Rossmann-like Domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / FLAVIN-ADENINE DINUCLEOTIDE / ISOPROPYL ALCOHOL / URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE / : ![]() | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ![]() ![]() ![]() ![]() | ||||||||||||
![]() | Wangkanont, K. / Kiessling, L.L. / Forest, K.T. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Substrate recognition by FAD in UDP-galactopyranose mutase Authors: Wangkanont, K. / Forest, K.T. / Kiessling, L.L. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 104 KB | Display | ![]() |
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PDB format | ![]() | 75.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 17.7 KB | Display | |
Data in CIF | ![]() | 25.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6d2eC ![]() 6d2gC ![]() 6d99C ![]() 6d9aC ![]() 6d9bC ![]() 6d9cC ![]() 6d9eC ![]() 5br7S 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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1 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 45737.668 Da / Num. of mol.: 1 / Fragment: UDP-galactopyranose mutase Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 202 molecules ![](data/chem/img/FAD.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/UD1.gif)
![](data/chem/img/IPA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/UD1.gif)
![](data/chem/img/IPA.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-FAD / | ||
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#3: Chemical | ChemComp-NA / | ||
#4: Chemical | ChemComp-UD1 / | ||
#5: Chemical | ChemComp-IPA / #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.37 Å3/Da / Density % sol: 63.46 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 100 mM Tris, 28% PEG400, 20% isopropanol |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 13, 2014 | ||||||||||||||||||||||||
Radiation | Monochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97856 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 2.2→38.923 Å / Num. obs: 60563 / % possible obs: 100 % / Redundancy: 29.2 % / Biso Wilson estimate: 42.49 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.018 / Rrim(I) all: 0.099 / Net I/σ(I): 24.3 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() | |||||||||
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Phasing MR |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5BR7 Resolution: 2.2→38.923 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 19.31
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 105.75 Å2 / Biso mean: 46.7024 Å2 / Biso min: 26.84 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.2→38.923 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10 / % reflection obs: 100 %
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