+Open data
-Basic information
Entry | Database: PDB / ID: 2yx4 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of T134A of ST1022 from Sulfolobus tokodaii | ||||||
Components | 150aa long hypothetical transcriptional regulator | ||||||
Keywords | TRANSCRIPTION REGULATOR / Transcriptional regulator / Lrp/AsnC family binding / ST1022 / 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 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.B. / Sakamoto, K. / Shinkai, A. / Kumar, P.K.R. / Yokoyama, S. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2yx4.cif.gz | 46.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2yx4.ent.gz | 32.9 KB | Display | PDB format |
PDBx/mmJSON format | 2yx4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2yx4_validation.pdf.gz | 440.1 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2yx4_full_validation.pdf.gz | 441.6 KB | Display | |
Data in XML | 2yx4_validation.xml.gz | 9.4 KB | Display | |
Data in CIF | 2yx4_validation.cif.gz | 12.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yx/2yx4 ftp://data.pdbj.org/pub/pdb/validation_reports/yx/2yx4 | HTTPS FTP |
-Related structure data
Related structure data | 2e7wSC 2e7xC 2efnC 2efoC 2efpC 2efqC 2pmhC 2pn6C 2yx7C S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| x 8||||||||
2 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 17468.447 Da / Num. of mol.: 1 / Mutation: T134A 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 |
---|---|
#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 |
---|
-Sample preparation
Crystal | Density Matthews: 2.89 Å3/Da / Density % sol: 57.37 % Preparation: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS. |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.2 Details: 20% PPG P400, 30% i-PrOH, 70mM Na3 Citrate, Hexamine cobalt(III)trichloride, pH 6.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 180 K |
---|---|
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→50 Å / Num. all: 26879 / Num. obs: 26879 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.3 % / Biso Wilson estimate: 16.9 Å2 / Rmerge(I) obs: 0.06 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.48 / Num. unique all: 2665 / % possible all: 99.9 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2E7W Resolution: 2→19.73 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 2260571.26 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS.
| ||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 56.2428 Å2 / ksol: 0.335601 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.6 Å2
| ||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→19.73 Å
| ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||
Xplor file |
|