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Open data
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Basic information
Entry | Database: PDB / ID: 6xhd | ||||||
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Title | Structure of Prolinyl-5'-O-adenosine phosphoramidate | ||||||
![]() | Ribonuclease pancreatic | ||||||
![]() | RNA BINDING PROTEIN / RNase A complex / amino acid release / prodrug | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Pallan, P.S. / Egli, M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: The Enzyme-Free Release of Nucleotides from Phosphoramidates Depends Strongly on the Amino Acid. Authors: Jovanovic, D. / Tremmel, P. / Pallan, P.S. / Egli, M. / Richert, C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 70.9 KB | Display | ![]() |
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PDB format | ![]() | 50.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 827.8 KB | Display | ![]() |
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Full document | ![]() | 833.9 KB | Display | |
Data in XML | ![]() | 16 KB | Display | |
Data in CIF | ![]() | 22.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6xhcC ![]() 6xheC ![]() 6xhfC ![]() 1afkS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 13708.326 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-K / | #3: Chemical | ChemComp-V2P / ( | #4: Chemical | ChemComp-MPD / ( | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.89 Å3/Da / Density % sol: 35.01 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: PROTEIN WAS CRYSTALLIZED FROM 25% PEG 3350, 20 MM SODIUM CITRATE, PH 5.5 Prolinyl-5'-O-adenosine phosphoramidate soaking was achieved as follows. 1 uL of a stock solution of 100 mM ligand ...Details: PROTEIN WAS CRYSTALLIZED FROM 25% PEG 3350, 20 MM SODIUM CITRATE, PH 5.5 Prolinyl-5'-O-adenosine phosphoramidate soaking was achieved as follows. 1 uL of a stock solution of 100 mM ligand was added to 2uL of reservoir solution, to achieve a concentration of ~33 mM in the soaking solution. A few RNase A crystals were soaked for 45 - 90 minutes in the soaking solution |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 19, 2019 / Details: C(111) |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97857 Å / Relative weight: 1 |
Reflection | Resolution: 1.51→50 Å / Num. obs: 31473 / % possible obs: 96.9 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.034 / Net I/σ(I): 25.76 |
Reflection shell | Resolution: 1.51→1.56 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.588 / Mean I/σ(I) obs: 1.38 / Num. unique obs: 2688 / Rpim(I) all: 0.372 / % possible all: 83 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1AFK (using one molecule) Resolution: 1.51→49.31 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.958 / SU B: 2.103 / SU ML: 0.073 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.085 / ESU R Free: 0.092 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
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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 max: 110.46 Å2 / Biso mean: 26.492 Å2 / Biso min: 14.4 Å2
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Refinement step | Cycle: final / Resolution: 1.51→49.31 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.512→1.551 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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