+Open data
-Basic information
Entry | Database: PDB / ID: 1mgw | ||||||
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Title | Crystal structure of RNase Sa3, cytotoxic microbial ribonuclease | ||||||
Components | Guanyl-specific ribonuclease Sa3 | ||||||
Keywords | HYDROLASE / alpha/beta protein / UB rolls | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Sevcik, J. / Urbanikova, L. / Leland, P.A. / Raines, R.T. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2002 Title: Links X-ray Structure of Two Crystalline Forms of a Streptomycete Ribonuclease with Cytotoxic Activity Authors: Sevcik, J. / Urbanikova, L. / Leland, P.A. / Raines, R.T. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2001 Title: Purification, crystallization and preliminary X-ray analysis of two crystal forms of ribonuclease Sa3 Authors: Hlinkova, V. / Urbanikova, L. / Krajcikova, D. / Sevcik, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1mgw.cif.gz | 53.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1mgw.ent.gz | 42.5 KB | Display | PDB format |
PDBx/mmJSON format | 1mgw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1mgw_validation.pdf.gz | 402.4 KB | Display | wwPDB validaton report |
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Full document | 1mgw_full_validation.pdf.gz | 402.3 KB | Display | |
Data in XML | 1mgw_validation.xml.gz | 7.8 KB | Display | |
Data in CIF | 1mgw_validation.cif.gz | 10.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mg/1mgw ftp://data.pdbj.org/pub/pdb/validation_reports/mg/1mgw | HTTPS FTP |
-Related structure data
Related structure data | 1mgrC 1rggS S: Starting model for refinement C: citing same article (ref.) |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 11057.126 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces aureofaciens (bacteria) / Strain: CCM3239 / Production host: Escherichia coli (E. coli) / References: UniProt: P30289, EC: 3.1.27.3 |
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#2: Chemical | ChemComp-LI / |
#3: 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: 3.8 Å3/Da / Density % sol: 68 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.6 Details: Tris, HCl, HEPES, lithium sulphate, pH 7.6, VAPOR DIFFUSION, HANGING DROP at 293K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 8.2 | |||||||||||||||||||||||||||||||||||||||||||||||||
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: X31 / Wavelength: 1.1 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 14, 2000 |
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→29.6 Å / Num. all: 11799 / Num. obs: 11799 / % possible obs: 100 % / Redundancy: 9.5 % / Biso Wilson estimate: 28.5 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 31.6 |
Reflection shell | Resolution: 2→2.02 Å / Redundancy: 7.9 % / Rmerge(I) obs: 0.306 / Mean I/σ(I) obs: 5.8 / Num. unique all: 390 / % possible all: 99.5 |
Reflection | *PLUS Highest resolution: 2 Å / % possible obs: 100 % / Rmerge(I) obs: 0.06 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1RGG Resolution: 2→29 Å / SU B: 8.861 / SU ML: 0.126 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.176 / ESU R Free: 0.125 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 25.813 Å2
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Refinement step | Cycle: LAST / Resolution: 2→29 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.02 Å /
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Refinement | *PLUS Highest resolution: 2 Å / Lowest resolution: 29.6 Å / Rfactor Rfree: 0.214 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: p_chiral_restr / Dev ideal target: 0.2 |