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Yorodumi- PDB-5zuy: Crystal structure of E134H mutant of phosphomannose isomerase fro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5zuy | ||||||
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Title | Crystal structure of E134H mutant of phosphomannose isomerase from Salmonella typhimurium | ||||||
Components | Mannose-6-phosphate isomerase | ||||||
Keywords | ISOMERASE / zinc binding / SUGAR BINDING PROTEIN | ||||||
Function / homology | Function and homology information mannose-6-phosphate isomerase / mannose-6-phosphate isomerase activity / GDP-mannose biosynthetic process / carbohydrate metabolic process / zinc ion binding / cytosol Similarity search - Function | ||||||
Biological species | Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Bangera, M. / Murthy, M.R.N. | ||||||
Funding support | India, 1items
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Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2019 Title: Structural and functional insights into phosphomannose isomerase: the role of zinc and catalytic residues. Authors: Bangera, M. / Gowda K, G. / Sagurthi, S.R. / Murthy, M.R.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5zuy.cif.gz | 170.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5zuy.ent.gz | 133 KB | Display | PDB format |
PDBx/mmJSON format | 5zuy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zu/5zuy ftp://data.pdbj.org/pub/pdb/validation_reports/zu/5zuy | HTTPS FTP |
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-Related structure data
Related structure data | 5zt4C 5zt5C 5zt6C 5zuwC 5zv0C 5zvrC 5zvuC 5zvxC 3h1mS 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
#1: Protein | Mass: 42799.723 Da / Num. of mol.: 1 / Mutation: E134H Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria) Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: manA, pmi, STM1467 / Production host: Escherichia coli (E. coli) / References: UniProt: P25081, mannose-6-phosphate isomerase | ||
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#2: Chemical | #3: 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: 2.18 Å3/Da / Density % sol: 43.48 % |
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Crystal grow | Temperature: 298 K / Method: microbatch / pH: 6.8 Details: 0.1 M Magnesium acetate tetrahydrate, 0.2 M Sodium cacodylate pH 6.8, 20% PEG 8000, 5% dioxane |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.95372 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 8, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95372 Å / Relative weight: 1 |
Reflection | Resolution: 2→37.15 Å / Num. obs: 26137 / % possible obs: 100 % / Redundancy: 8.7 % / Rsym value: 0.124 / Net I/σ(I): 12.9 |
Reflection shell | Resolution: 2→2.11 Å / Rsym value: 0.55 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3H1M Resolution: 2→37.15 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.911 / SU B: 9.238 / SU ML: 0.133 / Cross valid method: THROUGHOUT / ESU R: 0.193 / ESU R Free: 0.18 / 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: 23.364 Å2
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Refinement step | Cycle: 1 / Resolution: 2→37.15 Å
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Refine LS restraints |
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