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Yorodumi- PDB-3ukh: Crystal structure of udp-galactopyranose mutase from Aspergillus ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ukh | ||||||
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Title | Crystal structure of udp-galactopyranose mutase from Aspergillus fumigatus in complex with UDPGALP (non-reduced) | ||||||
Components | UDP-galactopyranose mutase | ||||||
Keywords | ISOMERASE / FLAVOENZYME / FAD / FADH2 ISOMERASE | ||||||
Function / homology | Function and homology information UDP-galactopyranose mutase / UDP-galactopyranose mutase activity / nucleotide binding Similarity search - Function | ||||||
Biological species | Aspergillus fumigatus (mold) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Van Straaten, K.E. / Sanders, D.A.R. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2012 Title: Structural Insight into the Unique Substrate Binding Mechanism and Flavin Redox State of UDP-galactopyranose Mutase from Aspergillus fumigatus. Authors: van Straaten, K.E. / Routier, F.H. / Sanders, D.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ukh.cif.gz | 856.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ukh.ent.gz | 706.4 KB | Display | PDB format |
PDBx/mmJSON format | 3ukh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ukh_validation.pdf.gz | 4.6 MB | Display | wwPDB validaton report |
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Full document | 3ukh_full_validation.pdf.gz | 4.8 MB | Display | |
Data in XML | 3ukh_validation.xml.gz | 178.4 KB | Display | |
Data in CIF | 3ukh_validation.cif.gz | 229.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uk/3ukh ftp://data.pdbj.org/pub/pdb/validation_reports/uk/3ukh | HTTPS FTP |
-Related structure data
Related structure data | 3ukaC 3ukfC 3ukkC 3uklC 3ukpC 3ukqC C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper:
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-Components
-Protein , 1 types, 8 molecules ABCDEFGH
#1: Protein | Mass: 58141.594 Da / Num. of mol.: 8 / Fragment: udpgalactopyranose mutase Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aspergillus fumigatus (mold) / Strain: CBS 144-89 / Gene: glf, glfA / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) GOLD / References: UniProt: Q4W1X2, UDP-galactopyranose mutase |
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-Non-polymers , 5 types, 1296 molecules
#2: Chemical | ChemComp-FAD / #3: Chemical | ChemComp-GDU / #4: Chemical | #5: Chemical | #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: 3.42 Å3/Da / Density % sol: 64.05 % |
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Crystal grow | Temperature: 295 K / pH: 8.5 Details: 0.1M Bis-Tris-Propane pH 8.5, 0.2M NaNO2, 20% PEG 3350, microbatch, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9795 |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 5, 2009 / Details: DOUBLE CRYSTAL MONOCHROMATOR |
Radiation | Monochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→35.548 Å / Num. obs: 266596 / % possible obs: 97.3 % / Observed criterion σ(I): 1 / Redundancy: 3.94 % / Rmerge(I) obs: 0.069 / Rsym value: 0.069 / Net I/σ(I): 8.6 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 3.85 % / Rmerge(I) obs: 0.432 / Mean I/σ(I) obs: 2.6 / % possible all: 88.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PARTIALLY REFINED MODEL FROM LMUGM Resolution: 2.3→35.548 Å / Occupancy max: 1 / Occupancy min: 0.35 / SU ML: 0.94 / Isotropic thermal model: Isotropic / σ(F): 1.96 / Phase error: 30.9 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.86 Å2 / ksol: 0.33 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.3→35.548 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell |
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