[English] 日本語
Yorodumi- PDB-1kh8: Structure of a cis-proline (P114) to glycine variant of Ribonuclease A -
+Open data
-Basic information
Entry | Database: PDB / ID: 1kh8 | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of a cis-proline (P114) to glycine variant of Ribonuclease A | ||||||
Components | pancreatic ribonuclease A | ||||||
Keywords | HYDROLASE / RNase A / ribonuclease A / proline / cis / trans / Cesium | ||||||
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 | Schultz, D.A. / Friedman, A.M. / White, M.A. / Fox, R.O. | ||||||
Citation | Journal: Protein Sci. / Year: 2005 Title: The crystal structure of the cis-proline to glycine variant (P114G) of ribonuclease A. Authors: Schultz, D.A. / Friedman, A.M. / White, M.A. / Fox, R.O. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1kh8.cif.gz | 38.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1kh8.ent.gz | 26 KB | Display | PDB format |
PDBx/mmJSON format | 1kh8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1kh8_validation.pdf.gz | 433.6 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1kh8_full_validation.pdf.gz | 434.2 KB | Display | |
Data in XML | 1kh8_validation.xml.gz | 7.6 KB | Display | |
Data in CIF | 1kh8_validation.cif.gz | 9.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kh/1kh8 ftp://data.pdbj.org/pub/pdb/validation_reports/kh/1kh8 | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 13799.459 Da / Num. of mol.: 1 / Mutation: P114G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Production host: Escherichia coli (E. coli) / References: UniProt: P61823, EC: 3.1.27.5 |
---|---|
#2: Chemical | ChemComp-SO4 / |
#3: Chemical | ChemComp-CS / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.96 Å3/Da / Density % sol: 37.09 % | |||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 303 K / Method: vapor diffusion, hanging drop / pH: 6.6 Details: NaPO4, CsCl2, ammonium sulfate, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 303K | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: unknown | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 288 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Details: mirrors |
Radiation | Monochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→30 Å / Num. all: 7592 / % possible obs: 94.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 0 / Biso Wilson estimate: 12.5 Å2 |
Reflection shell | Resolution: 2→2.03 Å / % possible all: 82.8 |
Reflection | *PLUS Lowest resolution: 30 Å / Num. obs: 7592 / Rmerge(I) obs: 0.053 |
-Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: High Salt Wild Type RNase A (PAUL: Kim, et al, Biochemistry 1992,31,12304-12314) Resolution: 2→30 Å / Isotropic thermal model: Isotropic / Cross valid method: throughout CNS refinement / σ(F): 2 / σ(I): 0 / Stereochemistry target values: Engh & Huber Details: X-PLOR refinement (6-2A) used for initial model building without CV set. Final rounds of model building (30-2A) were performed in CNS with a 5% CV set and several rounds of simulated ...Details: X-PLOR refinement (6-2A) used for initial model building without CV set. Final rounds of model building (30-2A) were performed in CNS with a 5% CV set and several rounds of simulated annealing to remove bias. Waters were picked using CNS after SA refinement. The sigma weighted R-factor (Rw) on all reflections is 18.0%.
| |||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.1 Å2
| |||||||||||||||||||||||||
Refine analyze |
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→30 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
LS refinement shell | Resolution: 2→2.03 Å / Rfactor Rfree error: 0.073
| |||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 30 Å | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
|