+Open data
-Basic information
Entry | Database: PDB / ID: 3aw9 | ||||||
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Title | Structure of UDP-galactose 4-epimerase mutant | ||||||
Components | NAD-dependent epimerase/dehydratase | ||||||
Keywords | ISOMERASE / Rossmann fold | ||||||
Function / homology | Function and homology information UDP-glucose 4-epimerase activity / galactose catabolic process via UDP-galactose / oxidoreductase activity / nucleotide binding / cytosol Similarity search - Function | ||||||
Biological species | Pyrobaculum calidifontis (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å | ||||||
Authors | Sakuraba, H. / Kawai, T. / Yoneda, K. / Ohshima, T. | ||||||
Citation | Journal: To be Published Title: Structure of UDP-galactose 4-epimerase mutant Authors: Sakuraba, H. / Kawai, T. / Yoneda, K. / Ohshima, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3aw9.cif.gz | 191.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3aw9.ent.gz | 158.4 KB | Display | PDB format |
PDBx/mmJSON format | 3aw9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3aw9_validation.pdf.gz | 2.2 MB | Display | wwPDB validaton report |
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Full document | 3aw9_full_validation.pdf.gz | 2.2 MB | Display | |
Data in XML | 3aw9_validation.xml.gz | 38.9 KB | Display | |
Data in CIF | 3aw9_validation.cif.gz | 52.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aw/3aw9 ftp://data.pdbj.org/pub/pdb/validation_reports/aw/3aw9 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 33864.934 Da / Num. of mol.: 3 / Mutation: DELETION MUTANT Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrobaculum calidifontis (archaea) / Strain: JCM 11548 / VA1 / Gene: Pcal_0885 / Plasmid: pET11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A3MUJ4 #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Sequence details | DELETION MUTANT, UNP RESIDUES 32-43 (NLSSGRREFVNP) OF THE NAD-BINDING LOOP OF THE WILD TYPE WERE ...DELETION MUTANT, UNP RESIDUES 32-43 (NLSSGRREFV | |
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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: 2.69 Å3/Da / Density % sol: 54.31 % |
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Crystal grow | Temperature: 293 K / Method: sitting drop / pH: 8 / Details: PEG 8000, pH 8.0, sitting drop, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 26, 2010 / Details: Rhodium coated silicon single crystal |
Radiation | Monochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→108.47 Å / Num. all: 48870 / Num. obs: 48870 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→50 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.931 / Occupancy max: 1 / Occupancy min: 0.25 / SU B: 6.662 / SU ML: 0.165 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.223 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 66.45 Å2 / Biso mean: 34.6108 Å2 / Biso min: 10.76 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.303→2.362 Å / Total num. of bins used: 20
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