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Open data
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Basic information
Entry | Database: PDB / ID: 1ucg | ||||||
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Title | Crystal structure of Ribonuclease MC1 N71T mutant | ||||||
![]() | Ribonuclease MC | ||||||
![]() | HYDROLASE / alpha plus beta | ||||||
Function / homology | ![]() ribonuclease T2 / ribonuclease T2 activity / RNA catabolic process / RNA binding / extracellular region Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Suzuki, A. / Numata, T. / Yao, M. / Tanaka, I. / Kimura, M. | ||||||
![]() | ![]() Title: Crystal structures of the ribonuclease MC1 mutants N71T and N71S in complex with 5'-GMP: structural basis for alterations in substrate specificity Authors: Numata, T. / Suzuki, A. / Kakuta, Y. / Kimura, K. / Yao, M. / Tanaka, I. / Yoshida, Y. / Ueda, T. / Kimura, M. #1: ![]() Title: Amino acid residues in ribonuclease MC1 from bitter gourd seeds which are essential for uridine specificity Authors: Numata, T. / Suzuki, A. / Yao, M. / Tanaka, I. / Kimura, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 90.8 KB | Display | ![]() |
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PDB format | ![]() | 68.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 367.9 KB | Display | ![]() |
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Full document | ![]() | 370.6 KB | Display | |
Data in XML | ![]() | 8.8 KB | Display | |
Data in CIF | ![]() | 13.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1j1fC ![]() 1j1gC ![]() 1bk7S S: Starting model for refinement C: citing same article ( |
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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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Unit cell |
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Details | There are two monomers in the asymmetric unit, each monomer is a biological unit. |
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Components
#1: Protein | Mass: 21198.033 Da / Num. of mol.: 2 / Mutation: N71T Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-MN / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 50.14 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: PEG 1540, Manganese Cloride tetrahydrate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: May 25, 2001 / Details: mirrors |
Radiation | Monochromator: Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→19.96 Å / Num. all: 50912 / Num. obs: 50884 / % possible obs: 99.2 % / Observed criterion σ(I): 3 / Redundancy: 7.6 % / Biso Wilson estimate: 36.31 Å2 / Rmerge(I) obs: 0.053 / Rsym value: 0.05 / Net I/σ(I): 9.1 |
Reflection shell | Resolution: 1.65→1.74 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.212 / Mean I/σ(I) obs: 3.8 / Num. unique all: 7159 / Rsym value: 0.189 / % possible all: 97.3 |
Reflection | *PLUS Lowest resolution: 35.81 Å / Num. obs: 50905 / Redundancy: 8.5 % / Num. measured all: 434769 |
Reflection shell | *PLUS % possible obs: 97.6 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 22.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1BK7 Resolution: 1.65→10 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 23.94 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.65→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.65→1.71 Å
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Refinement | *PLUS % reflection Rfree: 5 % / Rfactor Rfree: 0.195 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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