+Open data
-Basic information
Entry | Database: PDB / ID: 1z3l | ||||||
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Title | X-Ray Crystal Structure of a Mutant Ribonuclease S (F8Anb) | ||||||
Components |
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Keywords | HYDROLASE / RNase-S mutant (F8Anb) / S-Protein / S-Peptide / Cavity | ||||||
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: 1.8 Å | ||||||
Authors | Das, M. / Vasudeva Rao, B. / Ghosh, S. / Varadarajan, R. | ||||||
Citation | Journal: Biochemistry / Year: 2005 Title: Attempts to delineate the relative contributions of changes in hydrophobicity and packing to changes in stability of ribonuclease S mutants. Authors: Das, M. / Rao, B.V. / Ghosh, S. / Varadarajan, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1z3l.cif.gz | 38.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1z3l.ent.gz | 25.4 KB | Display | PDB format |
PDBx/mmJSON format | 1z3l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1z3l_validation.pdf.gz | 450.9 KB | Display | wwPDB validaton report |
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Full document | 1z3l_full_validation.pdf.gz | 452.5 KB | Display | |
Data in XML | 1z3l_validation.xml.gz | 7.7 KB | Display | |
Data in CIF | 1z3l_validation.cif.gz | 9.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z3/1z3l ftp://data.pdbj.org/pub/pdb/validation_reports/z3/1z3l | HTTPS FTP |
-Related structure data
Related structure data | 1z3mC 1z3pC 2rlnS C: citing same article (ref.) S: Starting model for refinement |
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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/peptide | Mass: 1672.837 Da / Num. of mol.: 1 / Mutation: F8AA3, M13NLE / Source method: obtained synthetically Details: S-Peptide containing the mutations was synthesized by solid phase peptide synthesis References: UniProt: P61823, EC: 3.1.27.5 | ||
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#2: Protein | Mass: 11555.981 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P61823, EC: 3.1.27.5 | ||
#3: Chemical | #4: 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: 2.1 Å3/Da / Density % sol: 41.48 % |
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Crystal grow | Temperature: 293 K / Method: batch method / pH: 5.75 Details: ammonium sulfate, cesium chloride, sodium acetate, pH 5.75, Batch method, temperature 293K |
-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Dec 5, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→20 Å / Num. all: 10932 / Num. obs: 10679 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 22 Å2 / Rmerge(I) obs: 0.071 |
Reflection shell | Resolution: 1.8→1.86 Å / Rmerge(I) obs: 0.208 / % possible all: 97 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2RLN Resolution: 1.8→14.97 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 888102.91 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 40.5132 Å2 / ksol: 0.389339 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.8 Å2 | ||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→14.97 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.89 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 7
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Xplor file |
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