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Open data
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Basic information
Entry | Database: PDB / ID: 1rnf | ||||||
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Title | X-RAY CRYSTAL STRUCTURE OF UNLIGANDED HUMAN RIBONUCLEASE 4 | ||||||
![]() | PROTEIN (RIBONUCLEASE 4) | ||||||
![]() | HYDROLASE / RIBONUCLEASE / PHOSPHODIESTERASE | ||||||
Function / homology | ![]() Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / ribonuclease A activity / RNA nuclease activity / antibacterial humoral response / nucleic acid binding / defense response to Gram-positive bacterium / extracellular space / extracellular region Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Terzyan, S.S. / Peracaula, R. / De Llorens, R. / Tsushima, Y. / Yamada, H. / Seno, M. / Gomis-Rueth, F.X. / Coll, M. | ||||||
![]() | ![]() Title: The three-dimensional structure of human RNase 4, unliganded and complexed with d(Up), reveals the basis for its uridine selectivity. Authors: Terzyan, S.S. / Peracaula, R. / de Llorens, R. / Tsushima, Y. / Yamada, H. / Seno, M. / 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 | ![]() | 63 KB | Display | ![]() |
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PDB format | ![]() | 46 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 375.1 KB | Display | ![]() |
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Full document | ![]() | 379.8 KB | Display | |
Data in XML | ![]() | 6.5 KB | Display | |
Data in CIF | ![]() | 10.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2rnfC ![]() 2ratS 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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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.518, 0.643, 0.564), Vector: |
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Components
#1: Protein | Mass: 13979.033 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P34096, Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 43.1 % | ||||||||||||||||||||
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Crystal grow | pH: 6.9 Details: 30% PEG4000, 0.1 M SODIUM CADODYLATE, PH 6.3, pH 6.9 | ||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||
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: IMAGE PLATE |
Radiation | Monochromator: GRAPHITE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→20 Å / Num. obs: 57662 / % possible obs: 97.7 % / Observed criterion σ(I): 2 / Redundancy: 4.3 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 8.2 |
Reflection shell | Resolution: 2.1→2.18 Å / Mean I/σ(I) obs: 2.56 / % possible all: 94.8 |
Reflection | *PLUS Num. obs: 13467 / Num. measured all: 57662 |
Reflection shell | *PLUS % possible obs: 94.8 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2RAT Resolution: 2.1→8 Å / σ(F): 2
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Refinement step | Cycle: LAST / Resolution: 2.1→8 Å
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Refine LS restraints |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.1 Å / Lowest resolution: 8 Å / σ(F): 2 / Num. reflection Rfree: 663 / % reflection Rfree: 6 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |