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Yorodumi- PDB-2pgx: Crystal structure of UPF0341 protein yhiQ from E. coli, Northeast... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2pgx | ||||||
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Title | Crystal structure of UPF0341 protein yhiQ from E. coli, Northeast Structural Genomics Target ER585 | ||||||
Components | UPF0341 protein yhiQ | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / alpha-beta protein / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG | ||||||
Function / homology | Function and homology information 16S rRNA (guanine1516-N2)-methyltransferase / rRNA (guanine-N2-)-methyltransferase activity / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli O157:H7 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å | ||||||
Authors | Forouhar, F. / Su, M. / Seetharaman, J. / Janjua, H. / Fang, Y. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. / Montelione, G.T. ...Forouhar, F. / Su, M. / Seetharaman, J. / Janjua, H. / Fang, Y. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG) | ||||||
Citation | Journal: To be Published Title: Crystal structure of UPF0341 protein yhiQ from Escherichia coli. Authors: Forouhar, F. / Su, M. / Seetharaman, J. / Janjua, H. / Fang, Y. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2pgx.cif.gz | 59.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2pgx.ent.gz | 46.6 KB | Display | PDB format |
PDBx/mmJSON format | 2pgx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2pgx_validation.pdf.gz | 418.5 KB | Display | wwPDB validaton report |
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Full document | 2pgx_full_validation.pdf.gz | 423 KB | Display | |
Data in XML | 2pgx_validation.xml.gz | 13 KB | Display | |
Data in CIF | 2pgx_validation.cif.gz | 18.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pg/2pgx ftp://data.pdbj.org/pub/pdb/validation_reports/pg/2pgx | HTTPS FTP |
-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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Unit cell |
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-Components
#1: Protein | Mass: 28338.742 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli O157:H7 (bacteria) / Species: Escherichia coli / Strain: EDL933, EHEC / Gene: yhiQ, Z4897, ECs4369 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: P68568 |
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#2: 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: 2.1 Å3/Da / Density % sol: 41.45 % Description: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS |
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Crystal grow | Temperature: 293 K / Method: microbatch under oil / pH: 8 Details: Protein solution: 20 mM Tris-HCl pH 7.5, 100 mM Sodium chloride, 5 mM DTT. Reservoir solution: 100 mM Tris-HCl pH 8.0, 20% PEG 20000, 100 mM Potassium acetate, MICROBATCH UNDER OIL, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97905 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 22, 2007 / Details: mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97905 Å / Relative weight: 1 |
Reflection | Resolution: 2→28.28 Å / Num. all: 32618 / Num. obs: 32618 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Biso Wilson estimate: 11.7 Å2 / Rmerge(I) obs: 0.071 / Rsym value: 0.058 / Net I/σ(I): 23.5 |
Reflection shell | Resolution: 2→2.08 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.375 / Mean I/σ(I) obs: 4.62 / Num. unique all: 3690 / Rsym value: 0.326 / % possible all: 99.1 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2→28.28 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 287497.29 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber Details: XtalView has also been used in refinement. THE FRIEDEL PAIRS WERE USED FOR PHASING
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 33.1668 Å2 / ksol: 0.306235 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→28.28 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.07 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 10
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