+Open data
-Basic information
Entry | Database: PDB / ID: 1z6d | ||||||
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Title | Ribonuclease A- IMP complex | ||||||
Components | Ribonuclease pancreaticPancreatic ribonuclease family | ||||||
Keywords | HYDROLASE / RIBONUCLEASE | ||||||
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 / FOURIER SYNTHESIS / Resolution: 1.54 Å | ||||||
Authors | Hatzopoulos, G.N. / Leonidas, D.D. / Kardakaris, R. / Kobe, J. / Oikonomakos, N.G. | ||||||
Citation | Journal: Febs J. / Year: 2005 Title: The binding of IMP to Ribonuclease A Authors: Hatzopoulos, G.N. / Leonidas, D.D. / Kardakaris, R. / Kobe, J. / Oikonomakos, N.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1z6d.cif.gz | 72.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1z6d.ent.gz | 53.7 KB | Display | PDB format |
PDBx/mmJSON format | 1z6d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z6/1z6d ftp://data.pdbj.org/pub/pdb/validation_reports/z6/1z6d | HTTPS FTP |
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-Related structure data
Related structure data | 1z6sC 1afuS 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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3 |
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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.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P61823, EC: 3.1.27.5 #2: Chemical | ChemComp-IMP / #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: 2.2 Å3/Da / Density % sol: 42.7 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 20mM sodium citrate, 20% PEG4000, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8115 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Feb 27, 2004 |
Radiation | Monochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8115 Å / Relative weight: 1 |
Reflection | Resolution: 1.54→60 Å / Num. all: 32622 / Num. obs: 32622 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 17.375 Å2 / Rsym value: 0.041 / Net I/σ(I): 18.7 |
Reflection shell | Resolution: 1.54→1.58 Å / Mean I/σ(I) obs: 7.6 / Rsym value: 0.199 / % possible all: 86 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: pdb entry 1afu Resolution: 1.54→19.1 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.931 / SU B: 1.518 / SU ML: 0.057 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.094 / ESU R Free: 0.099 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.37 Å2
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Refinement step | Cycle: LAST / Resolution: 1.54→19.1 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.538→1.578 Å / Total num. of bins used: 20
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