+Open data
-Basic information
Entry | Database: PDB / ID: 6xhe | ||||||
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Title | Structure of beta-prolinyl 5'-O-adenosine phosphoramidate | ||||||
Components | Ribonuclease pancreatic | ||||||
Keywords | RNA BINDING PROTEIN / RNase A complex / phosphoramidate structure | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å | ||||||
Authors | Pallan, P.S. / Egli, M. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2020 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6xhe.cif.gz | 66.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6xhe.ent.gz | 47.3 KB | Display | PDB format |
PDBx/mmJSON format | 6xhe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6xhe_validation.pdf.gz | 812.4 KB | Display | wwPDB validaton report |
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Full document | 6xhe_full_validation.pdf.gz | 817.1 KB | Display | |
Data in XML | 6xhe_validation.xml.gz | 13 KB | Display | |
Data in CIF | 6xhe_validation.cif.gz | 17.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xh/6xhe ftp://data.pdbj.org/pub/pdb/validation_reports/xh/6xhe | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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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.) Bos taurus (cattle) / Gene: RNASE1, RNS1 / Organ: Pancreas / Organ (production host): Pancreas / Production host: Bos taurus (cattle) / References: UniProt: P61823, pancreatic ribonuclease #2: Chemical | ChemComp-AMP / | #3: Chemical | ChemComp-V2J / | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.24 Å3/Da / Density % sol: 45.03 % |
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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, Glycinyl-5'-O-adenosine phosphoramidate soaking was achieved as follows. 1 uL of a stock solution of 50 mM ligand ...Details: PROTEIN WAS CRYSTALLIZED FROM 25% PEG 3350, 20 MM SODIUM CITRATE, PH 5.5, Glycinyl-5'-O-adenosine phosphoramidate soaking was achieved as follows. 1 uL of a stock solution of 50 mM ligand was added to 2uL of reservoir solution, to achieve a concentration of ~25 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: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97872 Å |
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Jul 10, 2019 / Details: C(111) |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 1.88→29.81 Å / Num. obs: 19587 / % possible obs: 98.2 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.094 / Rsym value: 0.094 / Net I/σ(I): 24.93 |
Reflection shell | Resolution: 1.88→1.97 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.951 / Num. unique obs: 1765 / Rsym value: 0.951 / % possible all: 89.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Single RNase molecule from PDB-ID Resolution: 1.88→29.81 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.932 / SU B: 6.451 / SU ML: 0.173 / Cross valid method: THROUGHOUT / ESU R: 0.176 / ESU R Free: 0.17 / 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: 43.318 Å2
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Refinement step | Cycle: 1 / Resolution: 1.88→29.81 Å
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