+Open data
-Basic information
Entry | Database: PDB / ID: 1w4o | ||||||
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Title | Binding of Nonnatural 3'-Nucleotides to Ribonuclease A | ||||||
Components | PANCREATIC RIBONUCLEASE A | ||||||
Keywords | HYDROLASE / RIBONUCLEASE A / NONATURAL 3'-NUCLEOTIDES / NUCLEASE / ENDONUCLEASE | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Jenkins, C.L. / Thiyagarajan, N. / Sweeney, R.Y. / Guy, M.P. / Kelemen, B.R. / Acharya, K.R. / Raines, R.T. | ||||||
Citation | Journal: FEBS J. / Year: 2005 Title: Binding of Non-Natural 3'-Nucleotides to Ribonuclease A Authors: Jenkins, C.L. / Thiyagarajan, N. / Sweeney, R.Y. / Guy, M.P. / Kelemen, B.R. / Acharya, K.R. / Raines, R.T. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1w4o.cif.gz | 67.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1w4o.ent.gz | 50.3 KB | Display | PDB format |
PDBx/mmJSON format | 1w4o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w4/1w4o ftp://data.pdbj.org/pub/pdb/validation_reports/w4/1w4o | HTTPS FTP |
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-Related structure data
Related structure data | 1w4pC 1w4qC 1afuS 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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-Components
#1: Protein | Mass: 13708.326 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: ARABINOURIDINE 3'-PHOSPHATE / Source: (natural) BOS TAURUS (cattle) / Organ: PANCREAS / References: UniProt: P61823, EC: 3.1.27.5 #2: Chemical | ChemComp-UA3 / | #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: 1.2 Å3/Da / Density % sol: 37.5 % |
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Crystal grow | pH: 5.5 Details: 20MM SODIUM CITRATE BUFFER, PH5.5, PEG 4000 (25% W/V), pH 5.50 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 1.488 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Feb 28, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.488 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. obs: 30191 / % possible obs: 89.9 % / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 26.1 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 10.8 |
Reflection shell | Resolution: 1.6→1.66 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 1.8 / % possible all: 88.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1AFU Resolution: 1.6→22.18 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 289831.89 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 43.4577 Å2 / ksol: 0.387518 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.6→22.18 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.7 Å / Rfactor Rfree error: 0.039 / Total num. of bins used: 6
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Xplor file |
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