+Open data
-Basic information
Entry | Database: PDB / ID: 1kf3 | ||||||
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Title | Atomic Resolution Structure of RNase A at pH 5.9 | ||||||
Components | pancreatic ribonucleasePancreatic ribonuclease family | ||||||
Keywords | HYDROLASE / RNase A / titration / pH / crystal / soaking | ||||||
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: 1.05 Å | ||||||
Authors | Berisio, R. / Sica, F. / Lamzin, V.S. / Wilson, K.S. / Zagari, A. / Mazzarella, L. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2002 Title: Atomic resolution structures of ribonuclease A at six pH values. Authors: Berisio, R. / Sica, F. / Lamzin, V.S. / Wilson, K.S. / Zagari, A. / Mazzarella, L. #1: Journal: J.Mol.Biol. / Year: 1999 Title: Protein titration in the crystal state Authors: Berisio, R. / Lamzin, V.S. / Sica, F. / Wilson, K.S. / Zagari, A. / Mazzarella, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1kf3.cif.gz | 75.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1kf3.ent.gz | 55.7 KB | Display | PDB format |
PDBx/mmJSON format | 1kf3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kf/1kf3 ftp://data.pdbj.org/pub/pdb/validation_reports/kf/1kf3 | HTTPS FTP |
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-Related structure data
Related structure data | 1kf2C 1kf4C 1kf5C 1kf7C 1kf8C 7rsaS 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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Unit cell |
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-Components
#1: Protein | Mass: 13708.326 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: PANCREAS / References: UniProt: P61823, EC: 3.1.27.5 |
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#2: Chemical | ChemComp-SO4 / |
#3: 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: 2.19 Å3/Da / Density % sol: 43.74 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: liquid diffusion / pH: 5.9 Details: 2-propanol, pH 5.9, LIQUID DIFFUSION, temperature 298K | ||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: batch method / Details: Tilton Jr., R.F., (1992) Biochemistry, 31, 2469. | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 |
Detector | Type: MARRESEARCH / Detector: AREA DETECTOR |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 1.05→30 Å / Num. all: 53498 / Num. obs: 53498 / % possible obs: 96.4 % / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Biso Wilson estimate: 12.1 Å2 / Rmerge(I) obs: 0.33 / Net I/σ(I): 18.9 |
Reflection shell | Resolution: 1.05→1.07 Å / Rmerge(I) obs: 0.345 / Mean I/σ(I) obs: 4.5 / Num. unique all: 2545 / % possible all: 92.9 |
Reflection | *PLUS Lowest resolution: 30 Å / Num. obs: 53494 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7rsa Resolution: 1.05→30 Å / Num. parameters: 11496 / Num. restraintsaints: 14435 / Stereochemistry target values: ENGH AND HUBER Details: Please note: ASUL 325 AND BHOH 168 ARE ALTERNATE CONFORMATIONS. CHOH 159 IS ALTERNATIVE ONLY TO THE A CONFORMER OF HIS119. CHOH 138 IS ALTERNATIVE ONLY TO THE A CONFORMER OF ASN 103.
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Solvent computation | Solvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-22 | ||||||||||||
Refine analyze | Num. disordered residues: 23 / Occupancy sum hydrogen: 893.75 / Occupancy sum non hydrogen: 1149.31 | ||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.05→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.05→1.09 Å /
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Software | *PLUS Name: SHELXL-96 / Classification: refinement | ||||||||||||
Refine LS restraints | *PLUS Type: s_chiral_restr / Dev ideal: 0.152 |