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Yorodumi- PDB-1lxj: X-RAY STRUCTURE OF YBL001c NORTHEAST STRUCTURAL GENOMICS (NESG) C... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1lxj | ||||||
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Title | X-RAY STRUCTURE OF YBL001c NORTHEAST STRUCTURAL GENOMICS (NESG) CONSORTIUM TARGET YTYst72 | ||||||
Components | HYPOTHETICAL 11.5KDA PROTEIN IN HTB2-NTH2 INTERGENIC REGION | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / Hypothetical protein / HTB2-NTH2 intergenic region / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å | ||||||
Authors | Tao, X. / Khayat, R. / Christendat, D. / Savchenko, A. / Xu, X. / Edwards, A. / Arrowsmith, C.H. / Tong, L. / Northeast Structural Genomics Consortium (NESG) | ||||||
Citation | Journal: Proteins / Year: 2003 Title: CRYSTAL STRUCTURES OF MTH1187 AND ITS YEAST ORTHOLOG YBL001C Authors: Tao, X. / Khayat, R. / Christendat, D. / Savchenko, A. / Xu, X. / Goldsmith-Fischman, S. / Honig, B. / Edwards, A. / Arrowsmith, C.H. / Tong, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1lxj.cif.gz | 34.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1lxj.ent.gz | 26.5 KB | Display | PDB format |
PDBx/mmJSON format | 1lxj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1lxj_validation.pdf.gz | 435.8 KB | Display | wwPDB validaton report |
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Full document | 1lxj_full_validation.pdf.gz | 437.1 KB | Display | |
Data in XML | 1lxj_validation.xml.gz | 9.2 KB | Display | |
Data in CIF | 1lxj_validation.cif.gz | 13 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lx/1lxj ftp://data.pdbj.org/pub/pdb/validation_reports/lx/1lxj | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 11676.963 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Production host: Escherichia coli (E. coli) / References: UniProt: P35195 |
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#2: Chemical | ChemComp-SO4 / |
#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: 3.25 Å3/Da / Density % sol: 62.1 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: Ammonium Sulfate, 2-METHYL-2,4-PENTANEDIOL, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 8.5 / Method: vapor diffusion | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97895 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: May 4, 2002 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97895 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→30 Å / Num. obs: 12726 / % possible obs: 86.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 16.5 Å2 |
Reflection shell | Resolution: 1.8→1.86 Å / % possible all: 85.7 |
Reflection | *PLUS Highest resolution: 1.8 Å / Num. measured all: 141589 / Rmerge(I) obs: 0.096 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.8→19.99 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 4329413.23 / Data cutoff high rms absF: 4329413.23 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Solvent computation | Bsol: 52.0701 Å2 / ksol: 0.351892 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→19.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.91 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 20 Å / Num. reflection obs: 13776 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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