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Yorodumi- PDB-2rnf: X-RAY CRYSTAL STRUCTURE OF HUMAN RIBONUCLEASE 4 IN COMPLEX WITH D(UP) -
+Open data
-Basic information
Entry | Database: PDB / ID: 2rnf | ||||||
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Title | X-RAY CRYSTAL STRUCTURE OF HUMAN RIBONUCLEASE 4 IN COMPLEX WITH D(UP) | ||||||
Components | RIBONUCLEASE 4 | ||||||
Keywords | HYDROLASE / RIBONUCLEASE / PHOSPHODIESTERASE | ||||||
Function / homology | Function and homology information 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Terzyan, S.S. / Peracaula, R. / De Llorens, R. / Tsushima, Y. / Yamada, H. / Seno, M. / Gomis-Ruth, F.X. / Coll, M. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1999 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2rnf.cif.gz | 64.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2rnf.ent.gz | 46.7 KB | Display | PDB format |
PDBx/mmJSON format | 2rnf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2rnf_validation.pdf.gz | 509.6 KB | Display | wwPDB validaton report |
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Full document | 2rnf_full_validation.pdf.gz | 517.9 KB | Display | |
Data in XML | 2rnf_validation.xml.gz | 7.5 KB | Display | |
Data in CIF | 2rnf_validation.cif.gz | 11.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rn/2rnf ftp://data.pdbj.org/pub/pdb/validation_reports/rn/2rnf | HTTPS FTP |
-Related structure data
Related structure data | 1rnfC 2ratS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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: |
-Components
#1: Protein | Mass: 13979.033 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) References: UniProt: P34096, Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 42.81 % | ||||||||||||||||||||
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Crystal grow | pH: 6.9 / Details: pH 6.9 | ||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS pH: 6.3 / 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: ROTATING ANODE / Type: RIGAKU RU200 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.4→20 Å / Num. all: 36143 / Num. obs: 36143 / % possible obs: 85.8 % / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Rmerge(I) obs: 0.134 / Net I/σ(I): 7.8 |
Reflection shell | Resolution: 2.4→2.49 Å / Mean I/σ(I) obs: 2.76 / % possible all: 89.2 |
Reflection | *PLUS Num. obs: 7980 / Num. measured all: 36143 |
Reflection shell | *PLUS % possible obs: 89.2 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2RAT Resolution: 2.4→8 Å / σ(F): 2
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Refinement step | Cycle: LAST / Resolution: 2.4→8 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.4 Å / Lowest resolution: 8 Å / σ(F): 2 / Num. reflection Rfree: 411 / % reflection Rfree: 6 % / Rfactor obs: 0.16 / Rfactor Rwork: 0.16 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |