+Open data
-Basic information
Entry | Database: PDB / ID: 6xhc | ||||||
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Title | Structure of glycinyl 5'-O-adenosine phosphoramidate | ||||||
Components | Ribonuclease pancreaticPancreatic ribonuclease family | ||||||
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: 1.6 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 | 6xhc.cif.gz | 67.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6xhc.ent.gz | 49.1 KB | Display | PDB format |
PDBx/mmJSON format | 6xhc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xh/6xhc ftp://data.pdbj.org/pub/pdb/validation_reports/xh/6xhc | HTTPS FTP |
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-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 | #3: 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: 2.18 Å3/Da / Density % sol: 43.68 % |
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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-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, Glycinyl-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-G / Wavelength: 0.97856 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 17, 2019 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97856 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.6→50 Å / Num. obs: 31715 / % possible obs: 99.4 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.024 / Rrim(I) all: 0.06 / Χ2: 1.455 / Net I/σ(I): 10.2 / Num. measured all: 184557 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: AFK1 Resolution: 1.6→41.6 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.946 / SU B: 2.163 / SU ML: 0.074 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.094 / ESU R Free: 0.103 / 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: 87.57 Å2 / Biso mean: 29.636 Å2 / Biso min: 16.34 Å2
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Refinement step | Cycle: final / Resolution: 1.6→41.6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.637 Å / Rfactor Rfree error: 0
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