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Yorodumi- PDB-5eqd: Structure of oxidized UDP-galactopyranose mutase from Mycobacteri... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5eqd | |||||||||
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Title | Structure of oxidized UDP-galactopyranose mutase from Mycobacterium smegmatis in complex with UDP in opened and closed form | |||||||||
Components | UDP-galactopyranose mutase | |||||||||
Keywords | ISOMERASE / galactofuranose | |||||||||
Function / homology | Function and homology information UDP-galactopyranose mutase / UDP-galactopyranose mutase activity / flavin adenine dinucleotide binding / metal ion binding / cytosol Similarity search - Function | |||||||||
Biological species | Mycobacterium smegmatis (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.83 Å | |||||||||
Authors | Wangkanont, K. / Kiessling, L.L. / Forest, K.T. | |||||||||
Funding support | United States, 2items
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Citation | Journal: to be published Title: Structural dynamics of UDP-galactopyranose mutase from Mycobacterium smegmatis Authors: Wangkanont, K. / Kiessling, L.L. / Forest, K.T. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5eqd.cif.gz | 195.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5eqd.ent.gz | 153.2 KB | Display | PDB format |
PDBx/mmJSON format | 5eqd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5eqd_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 5eqd_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 5eqd_validation.xml.gz | 38.2 KB | Display | |
Data in CIF | 5eqd_validation.cif.gz | 57.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eq/5eqd ftp://data.pdbj.org/pub/pdb/validation_reports/eq/5eqd | HTTPS FTP |
-Related structure data
Related structure data | 5er9C 5f3rC 1i8tS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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3 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 45875.906 Da / Num. of mol.: 2 / Fragment: residues 13-412 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium smegmatis (bacteria) / Strain: ATCC 700084 / mc(2)155 / Gene: glf, MSMEG_6404, MSMEI_6236 / Plasmid: pMAL c5x Details (production host): malE ORF in pMAL c5x was removed and replaced with the ORF for UDP-galactopyranose mutase Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0R629, UDP-galactopyranose mutase |
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-Non-polymers , 5 types, 756 molecules
#2: Chemical | #3: Chemical | ChemComp-NO3 / #4: Chemical | ChemComp-SO4 / #5: Chemical | ChemComp-UDP / | #6: 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: 3.03 Å3/Da / Density % sol: 59.46 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 100 mM Tris-HCl, 100 mM sodium nitrate, 1.8 M ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.978542 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 12, 2015 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.978542 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.83→50 Å / Num. obs: 96510 / % possible obs: 100 % / Redundancy: 7.2 % / Biso Wilson estimate: 24.63 Å2 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.035 / Rrim(I) all: 0.095 / Χ2: 1.125 / Net I/av σ(I): 23.269 / Net I/σ(I): 8.7 / Num. measured all: 699321 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1I8T Resolution: 1.83→45.8 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 20.45 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 89.22 Å2 / Biso mean: 29.4299 Å2 / Biso min: 14.36 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.83→45.8 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10
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