+Open data
-Basic information
Entry | Database: PDB / ID: 1hus | ||||||
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Title | RIBOSOMAL PROTEIN S7 | ||||||
Components | RIBOSOMAL PROTEIN S7 | ||||||
Keywords | RIBOSOMAL PROTEIN / RNA-BINDING PROTEIN / DECODING CENTER | ||||||
Function / homology | Function and homology information small ribosomal subunit / tRNA binding / rRNA binding / structural constituent of ribosome / translation Similarity search - Function | ||||||
Biological species | Geobacillus stearothermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD WITH SE-MET MUTANT / Resolution: 2.5 Å | ||||||
Authors | Hosaka, H. / Nakagawa, A. / Tanaka, I. | ||||||
Citation | Journal: Structure / Year: 1997 Title: Ribosomal protein S7: a new RNA-binding motif with structural similarities to a DNA architectural factor. Authors: Hosaka, H. / Nakagawa, A. / Tanaka, I. / Harada, N. / Sano, K. / Kimura, M. / Yao, M. / Wakatsuki, S. #1: Journal: J.Struct.Biol. / Year: 1997 Title: Crystallization and Preliminary X-Ray Crystallographic Study of the Ribosomal Protein S7 from Bacillus Stearothermophilus Authors: Harada, N. / Sano, K. / Kimura, M. / Hosaka, H. / Nakagawa, A. / Tanaka, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1hus.cif.gz | 36.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1hus.ent.gz | 28.6 KB | Display | PDB format |
PDBx/mmJSON format | 1hus.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hu/1hus ftp://data.pdbj.org/pub/pdb/validation_reports/hu/1hus | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 18230.283 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Geobacillus stearothermophilus (bacteria) Cell line: BL21 / Gene: S7 / Plasmid: BL21 / Gene (production host): S7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) LYSS / References: UniProt: P22744 |
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#2: 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: 2.9 Å3/Da / Density % sol: 57 % | ||||||||||||||||||||
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Crystal grow | pH: 8.2 Details: PROTEIN WAS CRYSTALLIZED FROM 0.1M NA HEPES BUFFER(PH8.2) WITH 4%(V/V) 2-PROPANOL AND 2.0M AMMONIUM SULFATE. | ||||||||||||||||||||
Crystal grow | *PLUS Method: unknown | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.90007 |
Detector | Type: PRINCETON 2K / Detector: CCD / Date: Mar 1, 1997 / Details: COLLIMATING AND FOCUSING MIRRORS |
Radiation | Monochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.90007 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→30 Å / Num. obs: 7586 / % possible obs: 97.6 % / Observed criterion σ(I): 18.7 / Redundancy: 2.8 % / Biso Wilson estimate: 33.3 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 20.3 |
Reflection shell | Resolution: 2.5→2.54 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.138 / Mean I/σ(I) obs: 5.8 / % possible all: 92.9 |
Reflection | *PLUS Num. measured all: 53236 |
Reflection shell | *PLUS % possible obs: 92.9 % |
-Processing
Software |
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Refinement | Method to determine structure: MAD WITH SE-MET MUTANT / Resolution: 2.5→8 Å / Rfactor Rfree error: 0.01 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Details: REFMAC (G.N.MURSHUDOV ET AL.) WAS ALSO USED DURING THE REFINEMENT CYCLE. PARAMETERS OF SE-MET WAS DERIVED FROM THOSE OF METHIONINE.
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Displacement parameters | Biso mean: 33.4 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.61 Å / Rfactor Rfree error: 0.038 / Total num. of bins used: 8
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.27 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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