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Yorodumi- PDB-2yx7: Crystals structure of T132A mutant of St1022 from sulfolobus toko... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2yx7 | ||||||
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Title | Crystals structure of T132A mutant of St1022 from sulfolobus tokodaii 7 | ||||||
Components | 150aa long hypothetical transcriptional regulator | ||||||
Keywords | TRANSCRIPTION / transcriptional regulator / st1022 / Lrp/AsnC family / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Sulfolobus tokodaii (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å | ||||||
Authors | Kumarevel, T.S. / Karthe, P. / Nakano, N. / Shinkai, A. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2008 Title: Crystal structure of glutamine receptor protein from Sulfolobus tokodaii strain 7 in complex with its effector L-glutamine: implications of effector binding in molecular association and DNA binding Authors: Kumarevel, T.S. / Nakano, N. / Ponnuraj, K. / Gopinath, S.C. / Sakamoto, K. / Shinkai, A. / Kumar, P.K. / Yokoyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2yx7.cif.gz | 45.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2yx7.ent.gz | 32.4 KB | Display | PDB format |
PDBx/mmJSON format | 2yx7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yx/2yx7 ftp://data.pdbj.org/pub/pdb/validation_reports/yx/2yx7 | HTTPS FTP |
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-Related structure data
Related structure data | 2e7wSC 2e7xC 2efnC 2efoC 2efpC 2efqC 2pmhC 2pn6C 2yx4C S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
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: 17468.447 Da / Num. of mol.: 1 / Mutation: T132A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfolobus tokodaii (archaea) / Gene: st1022 / Plasmid: BL21 (DE3) / Production host: Escherichia coli (E. coli) / References: UniProt: Q972W6, UniProt: F9VNT4*PLUS |
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#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-GLN / |
#4: 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: 2.87 Å3/Da / Density % sol: 57.15 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.2 Details: 20% PPG P400, 30% isopropanol, 70mM Sodium citrate, 210mM sorbitol, pH 6.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 180 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å |
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Mar 7, 2007 |
Radiation | Monochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→50 Å / Num. all: 12674 / Num. obs: 12674 / % possible obs: 97 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 13.1 % / Biso Wilson estimate: 21.4 Å2 / Rmerge(I) obs: 0.058 |
Reflection shell | Resolution: 2.05→2.12 Å / Redundancy: 11.1 % / Rmerge(I) obs: 0.444 / Num. unique all: 1097 / % possible all: 85.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2E7W Resolution: 2.05→20 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 2270358.28 / 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: 49.6985 Å2 / ksol: 0.324068 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 55.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.05→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.05→2.18 Å / Rfactor Rfree error: 0.038 / Total num. of bins used: 6
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Xplor file |
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