+Open data
-Basic information
Entry | Database: PDB / ID: 1te2 | ||||||
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Title | Putative Phosphatase Ynic from Escherichia coli K12 | ||||||
Components | 2-deoxyglucose-6-P phosphatase | ||||||
Keywords | HYDROLASE / Structural Genomics / Phosphatase / Phosphates / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | Function and homology information mannitol-1-phosphatase / sorbitol-6-phosphatase / 2-deoxyglucose-6-phosphatase / 2-deoxyglucose-6-phosphatase activity / mannitol-1-phosphatase activity / glucose-6-phosphatase activity / sorbitol-6-phosphatase activity / sugar-phosphatase / sugar-phosphatase activity / Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases ...mannitol-1-phosphatase / sorbitol-6-phosphatase / 2-deoxyglucose-6-phosphatase / 2-deoxyglucose-6-phosphatase activity / mannitol-1-phosphatase activity / glucose-6-phosphatase activity / sorbitol-6-phosphatase activity / sugar-phosphatase / sugar-phosphatase activity / Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / phosphatase activity / carbohydrate metabolic process / magnesium ion binding / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.76 Å | ||||||
Authors | Kim, Y. / Joachimiak, A. / Evdokimova, E. / Savchenko, A. / Edwards, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: Crystal Structure of Putative Phosphatase Ynic from Escherichia coli K12 Authors: Kim, Y. / Joachimiak, A. / Evdokimova, E. / Savchenko, A. / Edwards, A. | ||||||
History |
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Remark 600 | HETEROGEN AUTHOR STATED THAT THE MISSING ATOMS OF 2PL MAY BE DUE TO DISORDER. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1te2.cif.gz | 111.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1te2.ent.gz | 90.9 KB | Display | PDB format |
PDBx/mmJSON format | 1te2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/te/1te2 ftp://data.pdbj.org/pub/pdb/validation_reports/te/1te2 | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Details | unknown, but most likely a dimer as it is in the asymmetric unit. |
-Components
#1: Protein | Mass: 25068.719 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Plasmid: pET15 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: C3T7L2, UniProt: P77247*PLUS, phosphoglycolate phosphatase #2: Chemical | #3: Chemical | ChemComp-CA / #4: 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: 2.07 Å3/Da / Density % sol: 40.46 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.2 Details: Calcium Chloride PEG 3350 or PEGMME 3350, Sodium cacodylate, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794, 0.9795, 0.956 | ||||||||||||
Detector | Type: SBC-2 / Detector: CCD / Date: Feb 18, 2004 / Details: mirrors | ||||||||||||
Radiation | Monochromator: double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.76→25.16 Å / Num. all: 39931 / Num. obs: 38493 / % possible obs: 96 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.9 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 6.9 | ||||||||||||
Reflection shell | Resolution: 1.76→1.83 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 3.95 / Num. unique all: 2843 / % possible all: 71.2 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.76→25.16 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.936 / SU B: 3.238 / SU ML: 0.102 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.154 / ESU R Free: 0.14 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.716 Å2
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Refinement step | Cycle: LAST / Resolution: 1.76→25.16 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.76→1.809 Å / Total num. of bins used: 20
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