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Yorodumi- PDB-2apq: Crystal Structure of an Active Site Mutant of Bovine Pancreatic R... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2apq | ||||||
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Title | Crystal Structure of an Active Site Mutant of Bovine Pancreatic Ribonuclease A (H119A-RNase A) with a 10-Glutamine expansion in the C-terminal hinge-loop. | ||||||
Components | Ribonuclease | ||||||
Keywords | HYDROLASE / An active site mutant of RNase A (H119A) with an amyloidogenic expansion in the C-terminal hinge-loop region(between residues 112 and 113). | ||||||
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: 1.8 Å | ||||||
Authors | Sambashivan, S. / Liu, Y. / Sawaya, M.R. / Gingery, M. / Eisenberg, D. | ||||||
Citation | Journal: Nature / Year: 2005 Title: Amyloid-like fibrils of ribonuclease A with three-dimensional domain-swapped and native-like structure. Authors: Sambashivan, S. / Liu, Y. / Sawaya, M.R. / Gingery, 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 | 2apq.cif.gz | 40.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2apq.ent.gz | 27.2 KB | Display | PDB format |
PDBx/mmJSON format | 2apq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2apq_validation.pdf.gz | 413.7 KB | Display | wwPDB validaton report |
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Full document | 2apq_full_validation.pdf.gz | 413.7 KB | Display | |
Data in XML | 2apq_validation.xml.gz | 8.3 KB | Display | |
Data in CIF | 2apq_validation.cif.gz | 11.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ap/2apq ftp://data.pdbj.org/pub/pdb/validation_reports/ap/2apq | HTTPS FTP |
-Related structure data
Related structure data | 1fs3S 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: 15310.002 Da / Num. of mol.: 1 / Mutation: H119A - GQ10G expansion between G112 and N113 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Gene: RNASE1, RNS1 / Plasmid: pET32b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21-DE3 / 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: 2.74 Å3/Da / Density % sol: 55.1 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.3 Details: 0.4M Potassium Sodium tartrate tetrahydrate, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-D / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Apr 1, 2004 |
Radiation | Monochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→80 Å / Num. all: 14971 / Num. obs: 14971 / % possible obs: 94.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.4 % / Biso Wilson estimate: 28.3 Å2 / Rsym value: 0.057 / Net I/σ(I): 36.41 |
Reflection shell | Resolution: 1.8→1.86 Å / Mean I/σ(I) obs: 6.2 / Rsym value: 0.402 / % possible all: 91.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1fs3 Resolution: 1.8→58.22 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.948 / Cross valid method: THROUGHOUT / ESU R: 0.11 / ESU R Free: 0.11 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.763 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→58.22 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20
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