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Open data
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Basic information
Entry | Database: PDB / ID: 1i0v | ||||||
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Title | Ribonuclease T1 in complex with 2'GMP (form I crystal) | ||||||
![]() | GUANYL-SPECIFIC RIBONUCLEASE T1 | ||||||
![]() | HYDROLASE / ribonuclease / RNase / stability / metal binding / 2'GMP | ||||||
Function / homology | ![]() hyphal tip / ribonuclease T1 activity / ribonuclease T1 / cell septum / endonuclease activity / lyase activity / RNA binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | De Swarte, J. / De Vos, S. / Langhorst, U. / Steyaert, J. / Loris, R. | ||||||
![]() | ![]() Title: The contribution of metal ions to the conformational stability of ribonuclease T1: crystal versus solution. Authors: Deswarte, J. / De Vos, S. / Langhorst, U. / Steyaert, J. / Loris, R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 33.6 KB | Display | ![]() |
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PDB format | ![]() | 25.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 8.4 KB | Display | |
Data in CIF | ![]() | 11.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Protein | Mass: 11094.694 Da / Num. of mol.: 1 / Mutation: Q25K Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-CA / |
#3: Chemical | ChemComp-2GP / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.74 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.2 Details: MPD, acetaate, calcium chloride, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Details: Zegers, I., (1998) Nat. Struct. Biol., 5, 280. | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Details: graphite monochromator |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.23→35 Å / Num. all: 27338 / Num. obs: 27338 / % possible obs: 94.6 % / Observed criterion σ(F): -6 / Observed criterion σ(I): -3 / Redundancy: 5.54 % / Biso Wilson estimate: 11.18 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 16.54 |
Reflection shell | Resolution: 1.23→1.27 Å / Redundancy: 3.41 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 3.81 / Num. unique all: 2147 / % possible all: 75.4 |
Reflection | *PLUS Lowest resolution: 38 Å / Num. measured all: 151692 |
Reflection shell | *PLUS % possible obs: 75.4 % / Num. unique obs: 2147 / Num. measured obs: 7314 / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 3.48 |
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Processing
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Refinement | Method to determine structure: ![]()
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Refinement step | Cycle: LAST / Resolution: 1.234→35 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Version: 0.4 / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 35 Å / σ(F): 0 / Rfactor obs: 0.1783 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS |