+Open data
-Basic information
Entry | Database: PDB / ID: 1h8x | ||||||
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Title | Domain-swapped Dimer of a Human Pancreatic Ribonuclease Variant | ||||||
Components | RIBONUCLEASE 1 | ||||||
Keywords | HYDROLASE / RIBONUCLEASE / RNASE / HUMAN PANCREATIC RIBONUCLEASE / DOMAIN- SWAPPED DIMER | ||||||
Function / homology | Function and homology information pancreatic ribonuclease / ribonuclease A activity / RNA nuclease activity / Late endosomal microautophagy / Chaperone Mediated Autophagy / nucleic acid binding / lyase activity / defense response to Gram-positive bacterium / extracellular exosome Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Canals, A. / Pous, J. / Guasch, A. / Benito, A. / Ribo, M. / Vilanova, M. / Coll, M. | ||||||
Citation | Journal: Structure / Year: 2001 Title: The Structure of an Engineered Domain-Swapped Ribonuclease Dimer and its Implications for the Evolution of Proteins Toward Oligomerization Authors: Canals, A. / Pous, J. / Guasch, A. / Benito, A. / Ribo, M. / Vilanova, M. / Coll, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1h8x.cif.gz | 70.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1h8x.ent.gz | 52.4 KB | Display | PDB format |
PDBx/mmJSON format | 1h8x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1h8x_validation.pdf.gz | 370 KB | Display | wwPDB validaton report |
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Full document | 1h8x_full_validation.pdf.gz | 375 KB | Display | |
Data in XML | 1h8x_validation.xml.gz | 6.8 KB | Display | |
Data in CIF | 1h8x_validation.cif.gz | 11.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h8/1h8x ftp://data.pdbj.org/pub/pdb/validation_reports/h8/1h8x | HTTPS FTP |
-Related structure data
Related structure data | 1dzaS 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: 14454.169 Da / Num. of mol.: 2 / Fragment: RNASE 1, HP-RNASE / Mutation: YES Source method: isolated from a genetically manipulated source Details: RESIDIE 100 IS A FORMILMETHIONINE (FME) / Source: (gene. exp.) HOMO SAPIENS (human) / Description: SYNTHETIC GENE / Gene: PM8 / Organ: PANCREAS / Plasmid: PM8 / Gene (production host): PM8 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P07998, EC: 3.1.27.5 #2: Water | ChemComp-HOH / | Compound details | CHAIN A, B ENGINEERED | |
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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: 2.13 Å3/Da / Density % sol: 30 % | ||||||||||||||||||||||||
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Crystal grow | pH: 9 / Details: pH 9.00 | ||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 15, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→13 Å / Num. obs: 17315 / % possible obs: 99.4 % / Redundancy: 3.1 % / Biso Wilson estimate: 33.7 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 7.1 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.315 / Mean I/σ(I) obs: 2.4 / % possible all: 99.8 |
Reflection | *PLUS Highest resolution: 2 Å / Lowest resolution: 13 Å / Num. obs: 16247 / Redundancy: 3.4 % / Num. measured all: 56729 |
Reflection shell | *PLUS Highest resolution: 2 Å / Lowest resolution: 2.12 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1DZA Resolution: 2→12 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: DENSITY MODIFICATION | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.3 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→12 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.07 Å / Total num. of bins used: 10
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rwork: 0.27 |