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- PDB-8uay: Structure of Arginyl-5'-O-adenosine phosphoramidate/RNase A -

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Basic information

Entry
Database: PDB / ID: 8uay
TitleStructure of Arginyl-5'-O-adenosine phosphoramidate/RNase A
ComponentsRibonuclease pancreatic
KeywordsHYDROLASE / RNase-A / Nucleotide Prodrug / Amino Acidyl Phosphoramidate / Arginyl-5'-AMP / Phosphoramidate Hydrolysis / ProTide
Function / homology
Function and homology information


pancreatic ribonuclease / ribonuclease A activity / RNA nuclease activity / nucleic acid binding / defense response to Gram-positive bacterium / lyase activity / extracellular region
Similarity search - Function
Pancreatic ribonuclease / Ribonuclease A, active site / Ribonuclease A-domain / Ribonuclease A-like domain superfamily / Pancreatic ribonuclease / Pancreatic ribonuclease family signature. / Pancreatic ribonuclease
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / : / Ribonuclease pancreatic
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsPallan, P.S. / Egli, M.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research Foundation (DFG)364653263 Germany
Volkswagen FoundationAZ 92768 Germany
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2024
Title: Prolinyl Phosphoramidates of Nucleotides with Increased Reactivity.
Authors: Humboldt, A. / Rami, F. / Topp, F.M. / Arnold, D. / Gohringer, D. / Pallan, P.S. / Egli, M. / Richert, C.
History
DepositionSep 22, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribonuclease pancreatic
B: Ribonuclease pancreatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0264
Polymers27,4172
Non-polymers6102
Water2,270126
1
A: Ribonuclease pancreatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2122
Polymers13,7081
Non-polymers5031
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ribonuclease pancreatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8142
Polymers13,7081
Non-polymers1061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)99.508, 31.128, 68.575
Angle α, β, γ (deg.)90.00, 91.75, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Ribonuclease pancreatic / RNase 1 / RNase A


Mass: 13708.326 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P61823, pancreatic ribonuclease
#2: Chemical ChemComp-WF9 / (2S)-2-{[(R)-{[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl]amino}-5-carbamimidamidopentanoic acid (non-preferred name)


Mass: 503.407 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H26N9O8P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.94 Å3/Da / Density % sol: 36.47 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: PROTEIN WAS CRYSTALLIZED FROM 25 percent PEG 3350, 20 MM SODIUM CITRATE, PH 5.5. Arginyl-5'-O-adenosine phosphoramidate soaking was achieved as follows. 1 uL of a stock solution of 100 mM ...Details: PROTEIN WAS CRYSTALLIZED FROM 25 percent PEG 3350, 20 MM SODIUM CITRATE, PH 5.5. Arginyl-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 110 - 130 minutes in the soaking solution.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: LIQUID ANODE / Type: BRUKER METALJET / Wavelength: 1.3418 Å
DetectorType: Bruker PHOTON II / Detector: PIXEL / Date: Apr 25, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3418 Å / Relative weight: 1
ReflectionResolution: 1.8→16.76 Å / Num. obs: 19557 / % possible obs: 98.4 % / Redundancy: 4 % / Rmerge(I) obs: 0.112 / Net I/σ(I): 5.72
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 2.29 % / Rmerge(I) obs: 0.4874 / Mean I/σ(I) obs: 1.33 / Num. unique obs: 2711 / % possible all: 92.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
PROTEUM PLUSdata reduction
PROTEUM PLUSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→16.58 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.907 / SU B: 5.546 / SU ML: 0.161 / Cross valid method: THROUGHOUT / ESU R: 0.194 / ESU R Free: 0.18 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.28625 854 4.5 %RANDOM
Rwork0.22738 ---
obs0.22996 18100 95.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.01 Å2
Baniso -1Baniso -2Baniso -3
1--1.31 Å2-0 Å20.49 Å2
2--0.89 Å20 Å2
3---0.39 Å2
Refinement stepCycle: 1 / Resolution: 1.8→16.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1902 0 41 126 2069
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0121991
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1491.7032694
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.2175246
X-RAY DIFFRACTIONr_dihedral_angle_2_deg12.39758
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.69210336
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0870.2297
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021483
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.0612.739993
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.2084.9061236
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.2152.995998
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined7.86137.253192
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.459 47 -
Rwork0.384 1009 -
obs--73.03 %

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