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- PDB-1j1g: Crystal structure of the RNase MC1 mutant N71S in complex with 5'-GMP -
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Open data
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Basic information
Entry | Database: PDB / ID: 1j1g | ||||||
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Title | Crystal structure of the RNase MC1 mutant N71S in complex with 5'-GMP | ||||||
![]() | Ribonuclease MC1 | ||||||
![]() | HYDROLASE / Nucleic acid / RNA | ||||||
Function / homology | ![]() ribonuclease T2 / ribonuclease T2 activity / RNA catabolic process / RNA binding / extracellular region Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Numata, T. / Suzuki, A. / Kakuta, Y. / Kimura, K. / Yao, M. / Tanaka, I. / Yoshida, Y. / Ueda, T. / 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: Crystal structure of a ribonuclease from the seeds of bitter gourd (Momordica charantia) at 1.75 A resolution Authors: Nakagawa, A. / Tanaka, I. / Sakai, R. / Nakashima, T. / Funatsu, G. / Kimura, M. #2: ![]() Title: Crystal structures of the ribonuclease MC1 from bitter gourd seeds, complexed with 2'-UMP or 3'-UMP, reveal structural basis for uridine specificity Authors: Suzuki, A. / Yao, M. / Tanaka, I. / Numata, T. / Kikukawa, S. / Yamasaki, N. / Kimura, M. #3: ![]() 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 | ![]() | 57 KB | Display | ![]() |
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PDB format | ![]() | 40.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 11.5 KB | Display | |
Data in CIF | ![]() | 16.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1j1fC ![]() 1ucgC ![]() 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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Unit cell |
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Components
#1: Protein | Mass: 21184.992 Da / Num. of mol.: 1 / Mutation: N71S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 37.88 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.2M sodium acetate, 0.1M sodium cacodylate, 24% PEG8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: OXFORD / Detector: CCD / Date: Feb 1, 2002 / Details: mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→32.81 Å / Num. all: 25113 / Num. obs: 25113 / % possible obs: 95.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Biso Wilson estimate: 15.1 Å2 / Rmerge(I) obs: 0.157 / Net I/σ(I): 8.6 |
Reflection shell | Resolution: 1.6→1.66 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.233 / Mean I/σ(I) obs: 1.4 / Num. unique all: 1872 / % possible all: 72.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1BK7 Resolution: 1.6→32.81 Å / Rfactor Rfree error: 0.007 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 40.8682 Å2 / ksol: 0.368404 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.6→32.81 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.7 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
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Xplor file |
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