+Open data
-Basic information
Entry | Database: PDB / ID: 1aqp | ||||||
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Title | RIBONUCLEASE A COPPER COMPLEX | ||||||
Components | RIBONUCLEASE APancreatic ribonuclease family | ||||||
Keywords | HYDROLASE (PHOSPHORIC DIESTER) | ||||||
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: 2 Å | ||||||
Authors | Ramasubbu, N. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 1997 Title: Crystal structures of the copper and nickel complexes of RNase A: metal-induced interprotein interactions and identification of a novel copper binding motif. Authors: Balakrishnan, R. / Ramasubbu, N. / Varughese, K.I. / Parthasarathy, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1aqp.cif.gz | 42.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1aqp.ent.gz | 32.6 KB | Display | PDB format |
PDBx/mmJSON format | 1aqp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aq/1aqp ftp://data.pdbj.org/pub/pdb/validation_reports/aq/1aqp | HTTPS FTP |
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-Related structure data
Related structure data | 7rsaS 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 / Details: COPPER COMPLEX / Source: (natural) Bos taurus (cattle) / Organ: PANCREAS / References: UniProt: P61823, EC: 3.1.27.5 | ||
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#2: Chemical | #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: 2.18 Å3/Da / Density % sol: 45 % |
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Crystal grow | pH: 5.5 Details: ENZYME WAS CRYSTALLIZED FROM MPD WITH 6 MOLAR EXCESS OF COPPER, pH 5.5 |
Crystal grow | *PLUS Method: unknown |
-Data collection
Diffraction | Mean temperature: 287 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 1, 1996 / Details: COLLIMATOR |
Radiation | Monochromator: NI / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 6930 / % possible obs: 85 % / Observed criterion σ(I): 2 / Redundancy: 2.5 % / Rmerge(I) obs: 0.038 / Rsym value: 0.041 / Net I/σ(I): 13 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.08 / Mean I/σ(I) obs: 9 / Rsym value: 0.08 / % possible all: 55 |
Reflection shell | *PLUS % possible obs: 55 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 7RSA Resolution: 2→8 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.001 / σ(F): 2
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Displacement parameters | Biso mean: 18.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.3 Å / Luzzati d res low obs: 4 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→8 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.8 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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