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Yorodumi- PDB-2pkw: Crystal structure of UPF0341 protein yhiQ from Salmonella typhimu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2pkw | ||||||
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Title | Crystal structure of UPF0341 protein yhiQ from Salmonella typhimurium, Northeast Structural Genomics Consortium Target StR221 | ||||||
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 | Salmonella typhimurium LT2 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å | ||||||
Authors | Forouhar, F. / Su, M. / Seetharaman, J. / Fang, Y. / Xiao, R. / Cunningham, K. / Ma, L.-C. / Owens, L. / Liu, J. / Acton, T.B. ...Forouhar, F. / Su, M. / Seetharaman, J. / Fang, Y. / Xiao, R. / Cunningham, K. / Ma, L.-C. / Owens, L. / Liu, J. / 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 Salmonella typhimurium. Authors: Forouhar, F. / Su, M. / Seetharaman, J. / Fang, Y. / Xiao, R. / Cunningham, K. / Ma, L.-C. / Owens, L. / Liu, J. / 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 | 2pkw.cif.gz | 60.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2pkw.ent.gz | 47.9 KB | Display | PDB format |
PDBx/mmJSON format | 2pkw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pk/2pkw ftp://data.pdbj.org/pub/pdb/validation_reports/pk/2pkw | 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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Unit cell |
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-Components
#1: Protein | Mass: 28782.793 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella typhimurium LT2 (bacteria) Species: Salmonella typhimuriumSalmonella enterica subsp. enterica Strain: LT2, SGSC 1412 / Gene: yhiQ, STM3593 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: Q9X6G2 |
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#2: Chemical | ChemComp-TRS / |
#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: 1.99 Å3/Da / Density % sol: 38.21 % Description: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS |
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Crystal grow | Temperature: 291 K / Method: microbatch under oil / pH: 8 Details: 2 micro-L of protein solution containing 10 mM Tris-HCl pH 7.5, 100 mM Sodium chloride, 5 mM DTT was mixed with equal volume of 100 mM Tris-HCl pH 8.0, 40% PEG 1000, and 100 mM Magnesium ...Details: 2 micro-L of protein solution containing 10 mM Tris-HCl pH 7.5, 100 mM Sodium chloride, 5 mM DTT was mixed with equal volume of 100 mM Tris-HCl pH 8.0, 40% PEG 1000, and 100 mM Magnesium acetate, MICROBATCH UNDER OIL, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.9788 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 13, 2007 / Details: mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9788 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→28.53 Å / Num. all: 25710 / Num. obs: 25710 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Biso Wilson estimate: 16.2 Å2 / Rmerge(I) obs: 0.068 / Rsym value: 0.053 / Net I/σ(I): 28.1 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 6 % / Rmerge(I) obs: 0.329 / Mean I/σ(I) obs: 4 / Num. unique all: 2532 / Rsym value: 0.317 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.1→28.53 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 755895.08 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber Details: XtalView program has also been used in refinement. THE FRIEDEL PAIRS WERE USED FOR PHASING
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 40.8259 Å2 / ksol: 0.326574 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→28.53 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.23 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
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