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Open data
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Basic information
Entry | Database: PDB / ID: 1.0E+21 | ||||||
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Title | Ribonuclease 1 des1-7 Crystal Structure at 1.9A | ||||||
![]() | RIBONUCLEASE 1 | ||||||
![]() | HYDROLASE / HUMAN PANCREATIC RIBONUCLEASE | ||||||
Function / homology | ![]() pancreatic ribonuclease / ribonuclease A activity / RNA nuclease activity / Late endosomal microautophagy / Chaperone Mediated Autophagy / nucleic acid binding / lyase activity / defense response to Gram-positive bacterium / extracellular exosome Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Pous, J. / Mallorqui-Fernandez, G. / Peracaula, R. / Terzyan, S.S. / Futami, J. / Tada, H. / Yamada, H. / Seno, M. / De Llorens, R. / Gomis-Ruth, F.X. / Coll, M. | ||||||
![]() | ![]() Title: Three-Dimensional Crystal Structure of Human Rnase 1Dn7 at 1.9A Resolution Authors: Pous, J. / Mallorqui-Fernandez, G. / Peracaula, R. / Terzyan, S.S. / Futami, J. / Tada, H. / Yamada, H. / Seno, M. / De Llorens, R. / Gomis-Ruth, F.X. / Coll, 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 | ![]() | 40.1 KB | Display | ![]() |
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PDB format | ![]() | 27.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 363.6 KB | Display | ![]() |
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Full document | ![]() | 367.9 KB | Display | |
Data in XML | ![]() | 4.4 KB | Display | |
Data in CIF | ![]() | 6.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7rsaS S: Starting model for refinement |
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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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Components
#1: Protein | Mass: 14539.300 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / |
Compound details | CHAIN A AMINO-TERMINALLY |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.9 Å3/Da / Density % sol: 28 % | ||||||||||||||||||||
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Crystal grow | pH: 8.5 / Details: 7% PEG 8K, 0.1M TRIS-HCL PH 8.5 | ||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||
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 CCD / Detector: CCD / Date: Feb 15, 2000 Details: SAGITALLY FOCUSING GE(220 MULTILAYER TOROIDAL MIRROR |
Radiation | Monochromator: DIAMOND (111), GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→20 Å / Num. obs: 8618 / % possible obs: 92.9 % / Observed criterion σ(I): 2 / Redundancy: 3.2 % / Biso Wilson estimate: 18.8 Å2 / Rmerge(I) obs: 0.135 / Rsym value: 0.113 / Net I/σ(I): 4.4 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.426 / Mean I/σ(I) obs: 2 / Rsym value: 0.364 / % possible all: 87.2 |
Reflection | *PLUS Num. measured all: 27390 |
Reflection shell | *PLUS % possible obs: 87.2 % / Rmerge(I) obs: 0.364 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 7RSA Resolution: 1.9→20 Å / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0 / Details: RESIDUES 126, 127 AND 128 NOT SEEN IN DENSITY MAPS
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Solvent computation | Bsol: 50.93 Å2 / ksol: 0.34 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.496 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.99 Å / Total num. of bins used: 8
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.298 |