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Yorodumi- PDB-1n1x: Crystal Structure Analysis of the monomeric [S-carboxyamidomethyl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1n1x | ||||||
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Title | Crystal Structure Analysis of the monomeric [S-carboxyamidomethyl-Cys31, S-carboxyamidomethyl-Cys32] Bovine seminal ribonuclease | ||||||
Components | Ribonuclease, seminal | ||||||
Keywords | HYDROLASE | ||||||
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 / identical protein binding Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å | ||||||
Authors | Sica, F. / Di Fiore, A. / Zagari, A. / Mazzarella, L. | ||||||
Citation | Journal: Proteins / Year: 2003 Title: The unswapped chain of bovine seminal ribonuclease: Crystal structure of the free and liganded monomeric derivative Authors: Sica, F. / Di Fiore, A. / Zagari, A. / Mazzarella, L. #1: Journal: Acta Crystallogr.,Sect.D / Year: 1993 Title: Bovine seminal ribonuclease: structure at 1.9 A resolution Authors: Mazzarella, L. / Capasso, S. / Demasi, D. / Di Lorenzo, G. / Mattia, C.A. / Zagari, A. #2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1995 Title: Swapping structural determinants of ribonucleases: an energetic analysis of the hinge peptide 16-22 Authors: Mazzarella, L. / Vitagliano, L. / Zagari, A. #3: Journal: J.CRYST.GROWTH / Year: 1999 Title: Crystallization of multiple forms of bovine seminal ribonuclease in the liganded and unliganded state. Authors: Sica, F. / Adinolfi, S. / Berisio, R. / De Lorenzo, C. / Mazzarella, L. / Piccoli, R. / Vitagliano, L. / Zagari, A. #4: Journal: Eur.J.Biochem. / Year: 1995 Title: Assignment and secondary-structure determination of monomeric bovine seminal ribonuclease employing computer-assisted evaluation of homonuclear three-dimensional 1H-NMR spectra Authors: D'Ursi, A. / Oschkinat, H. / Cieslar, C. / Picone, D. / D'Alessio, G. / Amodeo, P. / Temussi, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1n1x.cif.gz | 35.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1n1x.ent.gz | 27.4 KB | Display | PDB format |
PDBx/mmJSON format | 1n1x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1n1x_validation.pdf.gz | 426.8 KB | Display | wwPDB validaton report |
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Full document | 1n1x_full_validation.pdf.gz | 427.7 KB | Display | |
Data in XML | 1n1x_validation.xml.gz | 8.8 KB | Display | |
Data in CIF | 1n1x_validation.cif.gz | 11.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n1/1n1x ftp://data.pdbj.org/pub/pdb/validation_reports/n1/1n1x | HTTPS FTP |
-Related structure data
Related structure data | 1n3zC 1bsrS 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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Unit cell |
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-Components
#1: Protein | Mass: 13746.742 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: seminal fluid / Source: (natural) Bos taurus (cattle) / References: UniProt: P00669, EC: 3.1.27.5 |
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#2: 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: 2.22 Å3/Da / Density % sol: 43.25 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.7 Details: PEG 4000, TRIS-HCl, sodium acetate, acetonitrile, glycerol (cryoprotectant), pH 8.7, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||||||||
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: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→18 Å / Num. all: 21157 / Num. obs: 21157 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 14.73 Å2 / Rmerge(I) obs: 0.028 / Net I/σ(I): 42 |
Reflection shell | Resolution: 1.45→1.47 Å / Rmerge(I) obs: 0.076 / Mean I/σ(I) obs: 17 / % possible all: 99.1 |
Reflection | *PLUS Num. measured all: 93751 |
Reflection shell | *PLUS % possible obs: 99.1 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1BSR Resolution: 1.45→18 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 17.8 Å2 | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.45→18 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.45→1.47 Å
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Refinement | *PLUS | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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