[English] 日本語
Yorodumi- PDB-2nrq: Crystal structure of protein SSO0741 from Sulfolobus solfataricus... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2nrq | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of protein SSO0741 from Sulfolobus solfataricus, Pfam DUF54 | ||||||
Components | Hypothetical protein ORF-c20_032Hypothesis | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / conserved hypothetical protein / Sulfolobus solfataricus / 10077c / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC | ||||||
Function / homology | Uncharacterised protein family UPF0201 / RNA binding / 50s Ribosomal Protein L5; Chain: A, / Ribosomal protein L5 / Ribosomal protein L5 domain superfamily / 2-Layer Sandwich / Alpha Beta / RNA-binding protein Function and homology information | ||||||
Biological species | Sulfolobus solfataricus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å | ||||||
Authors | Rao, K.N. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
Citation | Journal: Plos One / Year: 2008 Title: UPF201 archaeal specific family members reveal structural similarity to RNA-binding proteins but low likelihood for RNA-binding function. Authors: Rao, K.N. / Burley, S.K. / Swaminathan, S. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2nrq.cif.gz | 40.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2nrq.ent.gz | 28 KB | Display | PDB format |
PDBx/mmJSON format | 2nrq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nr/2nrq ftp://data.pdbj.org/pub/pdb/validation_reports/nr/2nrq | HTTPS FTP |
---|
-Related structure data
Related structure data | 2nwuC 2ogkC 2pzzC C: citing same article (ref.) |
---|---|
Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 18749.164 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Gene: ORF-c20_032 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UXC9 |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
---|
-Sample preparation
Crystal | Density Matthews: 2.57 Å3/Da / Density % sol: 52.19 % |
---|---|
Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7 Details: Sodium Formate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 290K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.1 |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 15, 2006 / Details: mirrors |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. all: 6695 / Num. obs: 6695 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.2 % / Biso Wilson estimate: 58.7 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 14.1 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.354 / Mean I/σ(I) obs: 3.5 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SAD / Resolution: 2.6→27.43 Å / Rfactor Rfree error: 0.02 / Data cutoff high absF: 173184.86 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber Details: the missing residues listed in Remark 465 are due to lack of electron density; Residues with missing atoms as listed in Remark 470 were modeled as ALA because of lack of electron density for side chain atoms.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 42.5155 Å2 / ksol: 0.346215 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.4 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→27.43 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.6→2.76 Å / Rfactor Rfree error: 0.054 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
|