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Yorodumi- PDB-2hf2: Domain shifting confirms monomeric structure of Escherichia sugar... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2hf2 | ||||||
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Title | Domain shifting confirms monomeric structure of Escherichia sugar phosphatase SUPH | ||||||
Components | Sugar phosphatase supH | ||||||
Keywords | HYDROLASE / HAD FAMILY / PHOSPHATASE / Structural Genomics / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC | ||||||
Function / homology | Function and homology information sorbitol-6-phosphatase activity / sugar-phosphatase / fructose-1-phosphatase activity / sugar-phosphatase activity / phosphatase activity / magnesium ion binding / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Patskovsky, Y. / Ramagopal, U. / Almo, S.C. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
Citation | Journal: To be Published Title: Domain Shifting Confirms Monomeric Structure of Escherichia Coli Sugar Phosphatase SupH Authors: Patskovsky, Y. / Ramagopal, U. / Almo, S.C. | ||||||
History |
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Remark 999 | SEQUENCE MSE -1 is a modified residue and a cloning artifact |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2hf2.cif.gz | 131.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2hf2.ent.gz | 101.9 KB | Display | PDB format |
PDBx/mmJSON format | 2hf2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hf/2hf2 ftp://data.pdbj.org/pub/pdb/validation_reports/hf/2hf2 | HTTPS FTP |
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-Related structure data
Related structure data | 1rlmS S: Starting model for refinement |
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Similar structure data | |
Other databases |
-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: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LEU / Beg label comp-ID: LEU / End auth comp-ID: ASN / End label comp-ID: ASN / Refine code: 1 / Auth seq-ID: 1 - 270 / Label seq-ID: 3 - 272
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-Components
#1: Protein | Mass: 32240.385 Da / Num. of mol.: 2 / Mutation: M1L, G45N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: SupH / Plasmid: pET / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P75792, sugar-phosphatase #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: 2.21 Å3/Da / Density % sol: 44.34 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: 20% PEG8000, 0.1 M SODIUM PHOSPHATE-CITRATE, 10% GLYCEROL, pH 4.50, VAPOR DIFFUSION, SITTING DROP, temperature 290K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 3, 2006 / Details: MIRRORS |
Radiation | Monochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. all: 42397 / Num. obs: 42397 / % possible obs: 95.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Rmerge(I) obs: 0.056 / Rsym value: 0.056 / Net I/σ(I): 13.4 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.323 / Mean I/σ(I) obs: 3.6 / Rsym value: 0.358 / % possible all: 73.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1RLM Resolution: 1.9→20 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.935 / SU B: 4.617 / SU ML: 0.134 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.186 / ESU R Free: 0.167 / 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: 35.808 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→20 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 2026 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 1.898→1.947 Å / Rfactor Rfree error: 0.052 / Total num. of bins used: 20
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