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Yorodumi- PDB-1ucd: Crystal structure of Ribonuclease MC1 from bitter gourd seeds com... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ucd | ||||||
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Title | Crystal structure of Ribonuclease MC1 from bitter gourd seeds complexed with 5'-UMP | ||||||
Components | Ribonuclease MC | ||||||
Keywords | HYDROLASE / alpha plus beta | ||||||
Function / homology | Function and homology information ribonuclease T2 / ribonuclease T2 activity / organic substance metabolic process / RNA binding Similarity search - Function | ||||||
Biological species | Momordica charantia (bitter melon) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å | ||||||
Authors | Suzuki, A. / Numata, T. / Yao, M. / Kimura, M. / Tanaka, I. | ||||||
Citation | Journal: To be published Title: Structure of RNase MC1 from bitter gourd seeds in complex with 5'UMP Authors: Suzuki, A. / Numata, T. / Yao, M. / Kimura, M. / Tanaka, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ucd.cif.gz | 57.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ucd.ent.gz | 39.9 KB | Display | PDB format |
PDBx/mmJSON format | 1ucd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uc/1ucd ftp://data.pdbj.org/pub/pdb/validation_reports/uc/1ucd | HTTPS FTP |
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-Related structure data
Related structure data | 1bk7S S: Starting model for refinement |
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Similar structure data |
-Links
-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. |
-Components
#1: Protein | Mass: 21227.010 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Momordica charantia (bitter melon) / Tissue: seed / References: UniProt: P23540, EC: 3.1.27.1 |
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#2: Chemical | ChemComp-U5P / |
#3: Chemical | ChemComp-URA / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 43.03 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.1 Details: PEG 8000, sodium acetate, sodium cacodylate, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.7 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Dec 21, 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: 1.3→19.8 Å / Num. all: 46033 / Num. obs: 45999 / % possible obs: 99.9 % / Observed criterion σ(I): 3 / Redundancy: 7.1 % / Biso Wilson estimate: 12.8 Å2 / Rmerge(I) obs: 0.052 / Rsym value: 0.048 / Net I/σ(I): 8.7 |
Reflection shell | Resolution: 1.3→1.37 Å / Redundancy: 7 % / Rmerge(I) obs: 0.239 / Mean I/σ(I) obs: 2.4 / Num. unique all: 6589 / Rsym value: 0.221 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1BK7 Resolution: 1.3→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: 17.53 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.3→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.3→1.35 Å
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