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Yorodumi- PDB-1iqv: Crystal Structure Analysis of the archaebacterial ribosomal protein S7 -
+Open data
-Basic information
Entry | Database: PDB / ID: 1iqv | ||||||
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Title | Crystal Structure Analysis of the archaebacterial ribosomal protein S7 | ||||||
Components | RIBOSOMAL PROTEIN S7 | ||||||
Keywords | RIBOSOME / RIBOSOMAL PROTEIN / RNA-BINDING / DECODING CENTER / HELIX-TURN-HELIX | ||||||
Function / homology | Function and homology information small ribosomal subunit / rRNA binding / structural constituent of ribosome / translation Similarity search - Function | ||||||
Biological species | Pyrococcus horikoshii (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Hosaka, H. / Yao, M. / Kimura, M. / Tanaka, I. | ||||||
Citation | Journal: J.Biochem. / Year: 2001 Title: The structure of the archaebacterial ribosomal protein S7 and its possible interaction with 16S rRNA. Authors: Hosaka, H. / Yao, M. / Kimura, M. / Tanaka, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1iqv.cif.gz | 48.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1iqv.ent.gz | 33.7 KB | Display | PDB format |
PDBx/mmJSON format | 1iqv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1iqv_validation.pdf.gz | 367.9 KB | Display | wwPDB validaton report |
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Full document | 1iqv_full_validation.pdf.gz | 370.5 KB | Display | |
Data in XML | 1iqv_validation.xml.gz | 4.9 KB | Display | |
Data in CIF | 1iqv_validation.cif.gz | 7.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iq/1iqv ftp://data.pdbj.org/pub/pdb/validation_reports/iq/1iqv | HTTPS FTP |
-Related structure data
Related structure data | 1husS S: Starting model for refinement |
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Similar 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: 25029.232 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Gene: PH1541 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: O59230 |
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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: 2.1 Å3/Da / Density % sol: 41.9 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: PEG3000, sodium chloride, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||||||||||||||
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: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å |
Detector | Type: OXFORD PX210 / Detector: CCD / Date: Mar 14, 2001 |
Radiation | Monochromator: Monochromator + Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→31 Å / Num. all: 14407 / Num. obs: 14407 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.7 % / Biso Wilson estimate: 41.4 Å2 / Rmerge(I) obs: 0.081 / Rsym value: 0.077 / Net I/σ(I): 7.2 |
Reflection shell | Resolution: 2.1→2.21 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.262 / Mean I/σ(I) obs: 2.9 / Num. unique all: 2048 / Rsym value: 0.243 / % possible all: 99.8 |
Reflection | *PLUS Lowest resolution: 40 Å / Num. measured all: 139697 |
Reflection shell | *PLUS % possible obs: 99.8 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1HUS Resolution: 2.1→10 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Solvent computation | Bsol: 66.8 Å2 / ksol: 0.436 e/Å3 | |||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.17 Å / Total num. of bins used: 10
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Xplor file | Serial no: 1 / Param file: protein_rep.param / Topol file: protein.top | |||||||||||||||||||||||||||
Software | *PLUS Name: CNS / Classification: refinement | |||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.1 Å / Lowest resolution: 10 Å / Num. reflection obs: 14240 / σ(F): 2 / % reflection Rfree: 10 % / Rfactor obs: 0.196 / Rfactor Rfree: 0.23 | |||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 35.7 Å2 | |||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.265 / % reflection Rfree: 10 % / Rfactor Rwork: 0.243 |