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- PDB-8uaz: Structure of Glutamyl-5'-O-adenosine phosphoramidate/RNase A -

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Basic information

Entry
Database: PDB / ID: 8uaz
TitleStructure of Glutamyl-5'-O-adenosine phosphoramidate/RNase A
ComponentsRibonuclease pancreatic
KeywordsHYDROLASE / RNase-A / Nucleotide Prodrug / Amino Acidyl Phosphoramidate / Glutamyl-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: 1.76 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)28,4755
Polymers27,4172
Non-polymers1,0593
Water1,74797
1
A: Ribonuclease pancreatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2913
Polymers13,7081
Non-polymers5822
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ribonuclease pancreatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1852
Polymers13,7081
Non-polymers4761
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)101.255, 32.957, 73.987
Angle α, β, γ (deg.)90.00, 90.43, 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-WFU / (2S)-2-{[(S)-{[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl]amino}pentanedioic acid (non-preferred name) / Glutamyl-5'-O-adenosine phosphoramidate


Mass: 476.335 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H21N6O10P / 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.: 97 / 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: 2.25 Å3/Da / Density % sol: 45.36 %
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. Glutaminyl-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. Glutaminyl-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 ~35 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: Jan 17, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3418 Å / Relative weight: 1
ReflectionResolution: 1.76→19.93 Å / Num. obs: 24382 / % possible obs: 98.9 % / Redundancy: 20 % / Rmerge(I) obs: 0.0949 / Net I/σ(I): 22.18
Reflection shellResolution: 1.76→1.86 Å / Redundancy: 7.08 % / Rmerge(I) obs: 0.701 / Mean I/σ(I) obs: 2.59 / Num. unique obs: 3478 / % possible all: 93.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
PROTEUM PLUSdata reduction
PROTEUM PLUSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.76→19.93 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.934 / SU B: 3.578 / SU ML: 0.107 / Cross valid method: THROUGHOUT / ESU R: 0.141 / ESU R Free: 0.135 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24935 1168 4.9 %RANDOM
Rwork0.20874 ---
obs0.21066 22845 97.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.693 Å2
Baniso -1Baniso -2Baniso -3
1--0.7 Å20 Å2-0.36 Å2
2---0.32 Å2-0 Å2
3---1.02 Å2
Refinement stepCycle: 1 / Resolution: 1.76→19.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1893 0 68 97 2058
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0121996
X-RAY DIFFRACTIONr_bond_other_d0.0030.0161761
X-RAY DIFFRACTIONr_angle_refined_deg1.1931.7222703
X-RAY DIFFRACTIONr_angle_other_deg0.4491.6254085
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7115245
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.31858
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.02710332
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0590.2301
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022315
X-RAY DIFFRACTIONr_gen_planes_other00.02441
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_it3.9613.121992
X-RAY DIFFRACTIONr_mcbond_other3.9613.126993
X-RAY DIFFRACTIONr_mcangle_it5.5125.5881233
X-RAY DIFFRACTIONr_mcangle_other5.4925.5861233
X-RAY DIFFRACTIONr_scbond_it4.9123.561004
X-RAY DIFFRACTIONr_scbond_other4.913.5591005
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.3676.3241471
X-RAY DIFFRACTIONr_long_range_B_refined8.80630.732211
X-RAY DIFFRACTIONr_long_range_B_other8.80330.662191
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.76→1.805 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.417 78 -
Rwork0.414 1352 -
obs--80.2 %

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