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Yorodumi- PDB-2e6e: Crystal structure of the stationary phase survival protein SurE f... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2e6e | ||||||
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Title | Crystal structure of the stationary phase survival protein SurE from Thermus thermophilus HB8 | ||||||
Components | 5'-nucleotidase surE | ||||||
Keywords | HYDROLASE / SurE protein | ||||||
Function / homology | Function and homology information 3'-nucleotidase activity / exopolyphosphatase activity / XMP 5'-nucleosidase activity / 5'-nucleotidase / nucleotide binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Iwasaki, W. / Miki, K. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2007 Title: Crystal Structure of the Stationary Phase Survival Protein SurE with Metal Ion and AMP Authors: Iwasaki, W. / Miki, K. | ||||||
History |
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Remark 300 | BIOMOLECULE 1 This entry contains the crystallographic asymmetric unit which consists of 4 chain(s) ...BIOMOLECULE 1 This entry contains the crystallographic asymmetric unit which consists of 4 chain(s) forming a tetramer. This protein is in a dimer-tetramer equilibrium in solution. It is unknown whether this protein is functional as a dimer or a tetramer. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2e6e.cif.gz | 174.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2e6e.ent.gz | 139.7 KB | Display | PDB format |
PDBx/mmJSON format | 2e6e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2e6e_validation.pdf.gz | 454.3 KB | Display | wwPDB validaton report |
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Full document | 2e6e_full_validation.pdf.gz | 476 KB | Display | |
Data in XML | 2e6e_validation.xml.gz | 32.9 KB | Display | |
Data in CIF | 2e6e_validation.cif.gz | 45 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e6/2e6e ftp://data.pdbj.org/pub/pdb/validation_reports/e6/2e6e | HTTPS FTP |
-Related structure data
Related structure data | 2e69C 2e6bC 2e6cSC 2e6gC 2e6hC C: citing same article (ref.) 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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Details | probably tetramer |
-Components
#1: Protein | Mass: 26625.287 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Plasmid: pET11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q53W92, 5'-nucleotidase #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: 2.07 Å3/Da / Density % sol: 40.45 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 4.2 Details: 30% ethylene glycol, 1% PEG4000, 0.1M Na acetate, pH 4.2, VAPOR DIFFUSION, temperature 293K |
-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å |
Detector | Type: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Dec 7, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. obs: 31508 / % possible obs: 96 % / Biso Wilson estimate: 30.6 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 26.9 |
Reflection shell | Resolution: 2.5→2.59 Å / Rmerge(I) obs: 0.133 / Mean I/σ(I) obs: 13.1 / % possible all: 80.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2E6C Resolution: 2.5→45.63 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 2100700.89 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 38.9254 Å2 / ksol: 0.355924 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→45.63 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
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Xplor file |
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