+Open data
-Basic information
Entry | Database: PDB / ID: 1js0 | ||||||
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Title | Crystal Structure of 3D Domain-swapped RNase A Minor Trimer | ||||||
Components | RIBONUCLEASE A | ||||||
Keywords | HYDROLASE / 3D domain swapping / RNase A | ||||||
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: 2.2 Å | ||||||
Authors | Liu, Y. / Gotte, G. / Libonati, M. / Eisenberg, D. | ||||||
Citation | Journal: Protein Sci. / Year: 2002 Title: Structures of the two 3D domain-swapped RNase A trimers. Authors: Liu, Y. / Gotte, G. / Libonati, M. / Eisenberg, D. #1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1998 Title: The Crystal Structure of a 3D Domain-swapped Dimer of RNase A at a 2.1 A Resolution Authors: Liu, Y. / Hart, P.J. / Schlunegger, M.P. / Eisenberg, D. #2: Journal: Nat.Struct.Biol. / Year: 2001 Title: A domain-swapped RNase A dimer with implications for amyloid formation Authors: Liu, Y. / Gotte, G. / Libonati, M. / Eisenberg, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1js0.cif.gz | 88.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1js0.ent.gz | 68.3 KB | Display | PDB format |
PDBx/mmJSON format | 1js0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1js0_validation.pdf.gz | 452 KB | Display | wwPDB validaton report |
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Full document | 1js0_full_validation.pdf.gz | 458 KB | Display | |
Data in XML | 1js0_validation.xml.gz | 19.2 KB | Display | |
Data in CIF | 1js0_validation.cif.gz | 27.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/js/1js0 ftp://data.pdbj.org/pub/pdb/validation_reports/js/1js0 | HTTPS FTP |
-Related structure data
Related structure data | 1rtbS 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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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.: 3 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: PANCREAS / References: UniProt: P61823, EC: 3.1.27.5 #2: Chemical | ChemComp-SO4 / #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: 2.28 Å3/Da / Density % sol: 46.13 % | ||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 3.7 Details: PEG 10,000, amonium sulfate, pH 3.7, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 6.7 | ||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1.072 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 10, 2001 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.072 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→100 Å / Num. all: 22989 / Num. obs: 22989 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 14 % / Biso Wilson estimate: 26 Å2 / Rsym value: 0.096 / Net I/σ(I): 18.6 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 5.6 % / Mean I/σ(I) obs: 4.4 / Num. unique all: 2250 / Rsym value: 0.412 / % possible all: 99.8 |
Reflection | *PLUS Lowest resolution: 40 Å / Num. measured all: 327545 / Rmerge(I) obs: 0.096 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1RTB Resolution: 2.2→10 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 21.9 Å2 | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.22 Å
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Refinement | *PLUS Lowest resolution: 10 Å / σ(F): 0 / % reflection Rfree: 10.9 % / Rfactor obs: 0.184 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 21.9 Å2 | |||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: c_angle_deg / Dev ideal: 1.906 | |||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.348 / Rfactor Rwork: 0.245 |