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Yorodumi- PDB-2gz6: Crystal Structure Of Anabaena sp. CH1 N-acetyl-D-glucosamine 2-ep... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2gz6 | ||||||
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Title | Crystal Structure Of Anabaena sp. CH1 N-acetyl-D-glucosamine 2-epimerase At 2.0 A | ||||||
Components | N-acetyl-D-glucosamine 2-epimerase | ||||||
Keywords | ISOMERASE / N-acetyl-D-glucosamine 2-epimerase / Anabaena sp. CH1 | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Anabaena sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Wang, W.C. / Wu, H.M. / Chang, Y.N. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2007 Title: The Central Cavity from the (Alpha/Alpha)(6) Barrel Structure of Anabaena sp. CH1 N-Acetyl-d-glucosamine 2-Epimerase Contains Two Key Histidine Residues for Reversible Conversion. Authors: Lee, Y.C. / Wu, H.M. / Chang, Y.N. / Wang, W.C. / Hsu, W.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2gz6.cif.gz | 177.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2gz6.ent.gz | 141 KB | Display | PDB format |
PDBx/mmJSON format | 2gz6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gz/2gz6 ftp://data.pdbj.org/pub/pdb/validation_reports/gz/2gz6 | HTTPS FTP |
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-Related structure data
Related structure data | 1fp3S S: Starting model for refinement |
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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
#1: Protein | Mass: 45108.137 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Anabaena sp. (bacteria) / Strain: CH1 / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: A4UA16, mannose-6-phosphate isomerase #2: 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: 2.3 Å3/Da / Density % sol: 46.61 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: Sodium Citrate, PEG3350, tert-butanol, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 113 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 20, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→30 Å / Num. obs: 57135 / % possible obs: 99.7 % |
Reflection shell | Resolution: 2→2.07 Å / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1FP3 Resolution: 2→24.82 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.931 / SU B: 3.901 / SU ML: 0.109 / Cross valid method: THROUGHOUT / ESU R: 0.171 / ESU R Free: 0.164 / 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 mean: 22.885 Å2
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Refinement step | Cycle: LAST / Resolution: 2→24.82 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20
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