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Yorodumi- PDB-3lxo: The crystal structure of ribonuclease A in complex with thymidine... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3lxo | ||||||
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Title | The crystal structure of ribonuclease A in complex with thymidine-3'-monophosphate | ||||||
Components | Ribonuclease pancreatic | ||||||
Keywords | HYDROLASE / ribonuclease A / RNA cleavage / nucleotides / enzyme catalysis / inhibitors / Disulfide bond / Endonuclease / Glycation / Glycoprotein / Nuclease / Secreted | ||||||
Function / homology | Function and homology information pancreatic ribonuclease / ribonuclease A activity / RNA nuclease activity / nucleic acid binding / lyase activity / defense response to Gram-positive bacterium / extracellular region Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.549 Å | ||||||
Authors | Doucet, N. / Jayasundera, T.B. / Simonovic, M. / Loria, J.P. | ||||||
Citation | Journal: Proteins / Year: 2010 Title: The crystal structure of ribonuclease A in complex with thymidine-3'-monophosphate provides further insight into ligand binding. Authors: Doucet, N. / Jayasundera, T.B. / Simonovic, M. / Loria, J.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3lxo.cif.gz | 61.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3lxo.ent.gz | 49.5 KB | Display | PDB format |
PDBx/mmJSON format | 3lxo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3lxo_validation.pdf.gz | 795.5 KB | Display | wwPDB validaton report |
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Full document | 3lxo_full_validation.pdf.gz | 797.2 KB | Display | |
Data in XML | 3lxo_validation.xml.gz | 9.2 KB | Display | |
Data in CIF | 3lxo_validation.cif.gz | 12.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lx/3lxo ftp://data.pdbj.org/pub/pdb/validation_reports/lx/3lxo | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 13708.326 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: pancreas / Source: (natural) Bos taurus (cattle) / References: UniProt: P61823, EC: 3.1.27.5 |
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#2: Chemical | ChemComp-T3P / |
#3: 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: 2.87 Å3/Da / Density % sol: 57.16 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 20% ammonium sulfate, 2M NaCl, pH 5.5., VAPOR DIFFUSION, HANGING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 294 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.514 Å |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Nov 14, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.514 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→70 Å / Num. all: 23146 / Num. obs: 23146 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Rsym value: 0.083 / Net I/σ(I): 18.1 |
Reflection shell | Resolution: 1.55→1.61 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 1.2 / Num. unique all: 2115 / % possible all: 91.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.549→28.954 Å / SU ML: 0.16 / σ(F): 2 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.654 Å2 / ksol: 0.402 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.549→28.954 Å
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Refine LS restraints |
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LS refinement shell |
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