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Yorodumi- PDB-1lni: CRYSTAL STRUCTURE ANALYSIS OF A RIBONUCLEASE FROM STREPTOMYCES AU... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1lni | ||||||
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Title | CRYSTAL STRUCTURE ANALYSIS OF A RIBONUCLEASE FROM STREPTOMYCES AUREOFACIENS AT ATOMIC RESOLUTION (1.0 A) | ||||||
Components | GUANYL-SPECIFIC RIBONUCLEASE SA | ||||||
Keywords | HYDROLASE / Ribonuclease Sa | ||||||
Function / homology | Function and homology information ribonuclease T1 activity / ribonuclease T1 / RNA endonuclease activity / lyase activity / RNA binding / extracellular region Similarity search - Function | ||||||
Biological species | Streptomyces aureofaciens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / STARTING MODEL WAS USED WITHOUT molecular replacement / Resolution: 1 Å | ||||||
Authors | Sevcik, J. / Lamzin, V.S. / Dauter, Z. / Wilson, K.S. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2002 Title: Atomic resolution data reveal flexibility in the structure of RNase Sa. Authors: Sevcik, J. / Lamzin, V.S. / Dauter, Z. / Wilson, K.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1lni.cif.gz | 116.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1lni.ent.gz | 89.2 KB | Display | PDB format |
PDBx/mmJSON format | 1lni.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ln/1lni ftp://data.pdbj.org/pub/pdb/validation_reports/ln/1lni | HTTPS FTP |
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-Related structure data
Related structure data | 1rggS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 10582.492 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces aureofaciens (bacteria) / Gene: U39467 / Plasmid: pEH100 / Production host: Escherichia coli (E. coli) / References: UniProt: P05798, EC: 3.1.27.3 #2: Chemical | ChemComp-SO4 / | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 48 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: ammonium sulfate, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||
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: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.934 Å |
Detector | Type: MARRESEARCH / Detector: AREA DETECTOR / Date: Aug 25, 1995 / Details: mirrors |
Radiation | Monochromator: triangular asymmetrically cut Si(111)or Ge(111) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 1→19.5 Å / Num. obs: 101141 / % possible obs: 97.5 % / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Biso Wilson estimate: 7.1 Å2 / Rmerge(I) obs: 0.042 / Net I/σ(I): 28.7 |
Reflection shell | Resolution: 1→1.02 Å / Rmerge(I) obs: 0.539 / Mean I/σ(I) obs: 2.4 / Num. unique all: 4660 / % possible all: 91.1 |
Reflection | *PLUS Num. obs: 101172 |
Reflection shell | *PLUS % possible obs: 91.1 % |
-Processing
Software |
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Refinement | Method to determine structure: STARTING MODEL WAS USED WITHOUT molecular replacement Starting model: PDB ENTRY 1RGG Resolution: 1→19.5 Å / Stereochemistry target values: Engh & Huber /
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Refinement step | Cycle: LAST / Resolution: 1→19.5 Å
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Software | *PLUS Name: SHELXL / Version: 93 / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.119 / Rfactor Rwork: 0.119 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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