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Open data
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Basic information
Entry | Database: PDB / ID: 1ch0 | ||||||
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Title | RNASE T1 VARIANT WITH ALTERED GUANINE BINDING SEGMENT | ||||||
![]() | PROTEIN (RIBONUCLEASE T1) | ||||||
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Function / homology | ![]() hyphal tip / ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Hoeschler, K. / Hoier, H. / Orth, P. / Hubner, B. / Saenger, W. / Hahn, U. | ||||||
![]() | ![]() Title: Structural analysis of an RNase T1 variant with an altered guanine binding segment. Authors: Hoschler, K. / Hoier, H. / Hubner, B. / Saenger, W. / Orth, P. / Hahn, U. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 77.8 KB | Display | ![]() |
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PDB format | ![]() | 57.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1rntS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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Components
#1: Protein | Mass: 11143.771 Da / Num. of mol.: 3 / Mutation: Q25K, K41E, Y42F, N43R, Y45W, E46Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() Strain (production host): PA2T1 (QUAAS EUR. J. BIOCHEM. V.173 PP.617-622) References: UniProt: P00651, EC: 3.1.27.3 #2: Chemical | ChemComp-CA / #3: Chemical | ![]() #4: Chemical | ChemComp-CL / | ![]() #5: Water | ChemComp-HOH / | ![]() Sequence details | THE PROTEIN USED IN THIS STUDY IS THE ISOZYME OF RIBONUCLEASE T1 WHERE A LYSINE RESIDUE REPLACES ...THE PROTEIN USED IN THIS STUDY IS THE ISOZYME OF RIBONUCLEA | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 36 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow![]() | pH: 7.7 Details: HANGING DROP CONTAINING 2.5 MG/ML RNASE T1, 2.5 MG/ML 2GMP, 15% PEG MONOMETHYLETHER 5000, 50 MM TRIS/HCL (PH7.7), 50 MM MGCL2, 50 MM CACL2 AGAINST 30 % PEG MONOMETHYLETHER 5000, 100 MM ...Details: HANGING DROP CONTAINING 2.5 MG/ML RNASE T1, 2.5 MG/ML 2GMP, 15% PEG MONOMETHYLETHER 5000, 50 MM TRIS/HCL (PH7.7), 50 MM MGCL2, 50 MM CACL2 AGAINST 30 % PEG MONOMETHYLETHER 5000, 100 MM TRIS/HCL (PH7.7), 100 MM MGCL2, 100 MM CACL2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 1, 1998 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.3→35.6 Å / Num. obs: 14434 / % possible obs: 97.7 % / Redundancy: 3.14 % / Biso Wilson estimate: 32.8 Å2 / Rsym value: 0.115 / Net I/σ(I): 9.04 |
Reflection shell | Resolution: 2.3→2.38 Å / Mean I/σ(I) obs: 2.8 / Rsym value: 0.396 / % possible all: 98.1 |
Reflection | *PLUS Rmerge(I) obs: 0.115 |
Reflection shell | *PLUS Highest resolution: 2.3 Å / % possible obs: 98.1 % / Rmerge(I) obs: 0.396 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 1RNT Resolution: 2.3→35.6 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Details: PARAMETER AND TOPOLOGY FILES FOR 2'GMP WERE OBTAINED FROM HTTP:// ALPHA2.BMC.UU.SE/HICUP/
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 31.9 Å2 / ksol: 0.324 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→35.6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.4 Å / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.4 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 35.6 Å / σ(F): 0 / % reflection Rfree: 5.6 % / Rfactor obs: 0.241 / Rfactor Rfree![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 34.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 2.4 Å / Rfactor Rfree: 0.287 / % reflection Rfree: 5.3 % / Rfactor Rwork: 0.254 |