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Open data
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Basic information
Entry | Database: PDB / ID: 1bk7 | ||||||
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Title | RIBONUCLEASE MC1 FROM THE SEEDS OF BITTER GOURD | ||||||
![]() | PROTEIN (RIBONUCLEASE MC1) | ||||||
![]() | HYDROLASE / HYDROLASE (NUCLEIC ACID / RNA) | ||||||
Function / homology | ![]() ribonuclease T2 / ribonuclease T2 activity / RNA catabolic process / RNA binding / extracellular region Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Nakagawa, A. / Tanaka, I. | ||||||
![]() | ![]() 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. #1: ![]() Title: Crystallization and Preliminary X-Ray Diffraction Analysis of a Plant Ribonuclease from the Seeds of the Bitter Gourd Momordica Charantia Authors: De, A. / Funatsu, G. #2: ![]() Title: The Complete Amino Acid Sequence of Ribonuclease from the Seeds of Bitter Gourd Authors: Ide, H. / Kimura, M. / Arai, M. / Funatsu, G. #3: ![]() Title: The Complete Amino Acid Sequence of Ribonuclease from the Seeds of Bitter Gourd Authors: Ide, H. / Kimura, M. / Arai, M. / Funatsu, G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 52.3 KB | Display | ![]() |
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PDB format | ![]() | 37.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 421.6 KB | Display | ![]() |
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Full document | ![]() | 423.1 KB | Display | |
Data in XML | ![]() | 11 KB | Display | |
Data in CIF | ![]() | 15.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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: 21227.010 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47 % |
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Crystal grow | pH: 6.7 Details: PROTEN WAS CRYSTALLIZED FROM THE 1:1 MIXTURE OF 10MG/ML PROTEIN SOLUTION IN 5MM TRIS-HCL PH7.2 AND 30% PEG 6000, 0.2M NA-ACETATE, 0.1M NA-CACODYLATE PH 6.7 |
Crystal grow | *PLUS Method: other / Details: De, A., (1991) J. Mol. Biol., 228, 1271. |
-Data collection
Diffraction | Mean temperature: 283 K |
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Diffraction source | Source: ![]() |
Detector | Type: MACSCIENCE / Detector: IMAGE PLATE / Date: Feb 15, 1996 / Details: MIRRORS |
Radiation | Monochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Highest resolution: 1.75 Å / Num. obs: 69704 / % possible obs: 98.4 % / Observed criterion σ(I): 4 / Redundancy: 3.4 % / Biso Wilson estimate: 16.3 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 9.1 |
Reflection shell | Resolution: 1.75→1.95 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.199 / Mean I/σ(I) obs: 3.5 / % possible all: 98.2 |
Reflection | *PLUS Num. obs: 20323 / Num. measured all: 69704 |
Reflection shell | *PLUS % possible obs: 98.2 % |
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Processing
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Refinement | Method to determine structure: ![]()
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Displacement parameters | Biso mean: 19.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.75→100 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.75→1.86 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 100 Å / σ(F): 0 / % reflection Rfree: 5.1 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 19.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.364 / % reflection Rfree: 5.2 % / Rfactor Rwork: 0.327 |