+Open data
-Basic information
Entry | Database: PDB / ID: 6xhf | ||||||
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Title | Structure of Phenylalanyl-5'-O-adenosine phosphoramidate | ||||||
Components | Ribonuclease pancreatic | ||||||
Keywords | RNA BINDING PROTEIN / RNase A complex / amino acid release / prodrug | ||||||
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: 1.45 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 | 6xhf.cif.gz | 68.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6xhf.ent.gz | 49.1 KB | Display | PDB format |
PDBx/mmJSON format | 6xhf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6xhf_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 6xhf_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 6xhf_validation.xml.gz | 14.7 KB | Display | |
Data in CIF | 6xhf_validation.cif.gz | 19.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xh/6xhf ftp://data.pdbj.org/pub/pdb/validation_reports/xh/6xhf | HTTPS FTP |
-Related structure data
Related structure data | 6xhcC 6xhdC 6xheC 1afkS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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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 / Production host: Bos taurus (cattle) / References: UniProt: P61823, pancreatic ribonuclease #2: Chemical | #3: Chemical | #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: 2.16 Å3/Da / Density % sol: 43.16 % |
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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 Phenylalanyl-O5'-adenosine phosphoramidate was soaked into the crystals using a stock solution of 100 mM, to achieve ...Details: PROTEIN WAS CRYSTALLIZED FROM 25% PEG 3350, 20 MM SODIUM CITRATE, PH 5.5 Phenylalanyl-O5'-adenosine phosphoramidate was soaked into the crystals using a stock solution of 100 mM, to achieve ~35 mM 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-F / Wavelength: 0.97872 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Jul 10, 2019 / Details: Be (Beryllium lens) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.45→50 Å / Num. obs: 41463 / % possible obs: 98 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.031 / Rrim(I) all: 0.083 / Χ2: 1.644 / Net I/σ(I): 9.2 / Num. measured all: 271958 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: One molecule from PDB ID 1AFK Resolution: 1.45→30.93 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.956 / SU B: 2.005 / SU ML: 0.072 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.076 / ESU R Free: 0.08 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 98.14 Å2 / Biso mean: 30.032 Å2 / Biso min: 11.64 Å2
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Refinement step | Cycle: final / Resolution: 1.45→30.93 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.45→1.485 Å / Rfactor Rfree error: 0
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