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Yorodumi- PDB-6d9a: Crystal structure of Corynebacterium diphtheriae UDP-galactopyran... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6d9a | ||||||||||||
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Title | Crystal structure of Corynebacterium diphtheriae UDP-galactopyranose mutase in complex with UDP-GalNAc (open, reduced) | ||||||||||||
Components | UDP-galactopyranose mutase | ||||||||||||
Keywords | 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 / DIHYDROFLAVINE-ADENINE DINUCLEOTIDE / ISOPROPYL ALCOHOL / URIDINE-DIPHOSPHATE-N-ACETYLGALACTOSAMINE / : Function and homology information | ||||||||||||
Biological species | Corynebacterium diphtheriae (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.9 Å | ||||||||||||
Authors | Wangkanont, K. / Kiessling, L.L. / Forest, K.T. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: To be published 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6d9a.cif.gz | 99.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6d9a.ent.gz | 72.1 KB | Display | PDB format |
PDBx/mmJSON format | 6d9a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d9/6d9a ftp://data.pdbj.org/pub/pdb/validation_reports/d9/6d9a | HTTPS FTP |
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-Related structure data
Related structure data | 6d2eC 6d2gC 6d99C 6d9bC 6d9cC 6d9dC 6d9eC 5br7S S: Starting model for refinement C: citing same article (ref.) |
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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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-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.) Corynebacterium diphtheriae (bacteria) / Gene: BU167_07490 / Plasmid: modified pMAL C5x / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A246CDW5 |
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-Non-polymers , 5 types, 22 molecules
#2: Chemical | ChemComp-NA / |
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#3: Chemical | ChemComp-FDA / |
#4: Chemical | ChemComp-UD2 / |
#5: Chemical | ChemComp-IPA / |
#6: 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: 3.34 Å3/Da / Density % sol: 63.14 % |
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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: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å | ||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 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: 0.97872 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 2.9→48.72 Å / Num. obs: 26212 / % possible obs: 100 % / Redundancy: 27.8 % / Biso Wilson estimate: 69.02 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.121 / Rpim(I) all: 0.023 / Rrim(I) all: 0.123 / Net I/σ(I): 22.5 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5BR7 Resolution: 2.9→47.009 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.12
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 122.39 Å2 / Biso mean: 63.0951 Å2 / Biso min: 27.81 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.9→47.009 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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