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- PDB-1ucc: Crystal structure of the Ribonuclease MC1 from bitter gourd seeds... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1ucc | ||||||
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Title | Crystal structure of the Ribonuclease MC1 from bitter gourd seeds complexed with 3'-UMP. | ||||||
![]() | 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. / Yao, M. / Tanaka, I. / Numata, T. / Kikukawa, S. / Yamasaki, N. / Kimura, M. | ||||||
![]() | ![]() 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. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 52.5 KB | Display | ![]() |
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PDB format | ![]() | 36.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 436.3 KB | Display | ![]() |
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Full document | ![]() | 439.1 KB | Display | |
Data in XML | ![]() | 6.1 KB | Display | |
Data in CIF | ![]() | 8.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1ucaC ![]() 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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Unit cell |
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Details | The bilogical unit is a monomer in the asymmetric unit. |
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Components
#1: Protein | Mass: 21227.010 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#2: Chemical | ChemComp-U3P / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.28 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.7 Details: PEG 8000, sodium acetate, sodium cacodylate, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||||||||
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: CCD / Date: Oct 12, 1999 / Details: mirrors |
Radiation | Monochromator: Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.7 Å / Relative weight: 1 |
Reflection | Resolution: 1.77→19.49 Å / Num. all: 28892 / Num. obs: 18370 / % possible obs: 92.7 % / Observed criterion σ(I): 3 / Redundancy: 4.3 % / Biso Wilson estimate: 15.729 Å2 / Rmerge(I) obs: 0.086 / Rsym value: 0.076 / Net I/σ(I): 6.6 |
Reflection shell | Resolution: 1.77→1.87 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.369 / Mean I/σ(I) obs: 2 / Num. unique all: 2684 / Rsym value: 0.33 / % possible all: 94.3 |
Reflection | *PLUS Lowest resolution: 19.4 Å / Num. measured all: 427770 |
Reflection shell | *PLUS % possible obs: 94.3 % / Rmerge(I) obs: 0.37 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1BK7 Resolution: 1.77→10 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 18.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.77→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.77→1.83 Å
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Refinement | *PLUS Num. reflection obs: 18243 / % reflection Rfree: 5 % | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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