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- PDB-8ub1: Structure of Butyl-5'-O-adenosine phosphoramidate/RNase A -

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Basic information

Entry
Database: PDB / ID: 8ub1
TitleStructure of Butyl-5'-O-adenosine phosphoramidate/RNase A
ComponentsRibonuclease pancreatic
KeywordsHYDROLASE / RNase-A / Nucleotide Prodrug / Amino Acidyl Phosphoramidate / Butyl-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
: / Ribonuclease pancreatic
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.53 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)27,8193
Polymers27,4172
Non-polymers4021
Water2,594144
1
A: Ribonuclease pancreatic


Theoretical massNumber of molelcules
Total (without water)13,7081
Polymers13,7081
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ribonuclease pancreatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1112
Polymers13,7081
Non-polymers4021
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.027, 32.123, 72.425
Angle α, β, γ (deg.)90.00, 90.71, 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-WFL / 5'-O-[(R)-(butylamino)(hydroxy)phosphoryl]adenosine


Mass: 402.343 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H23N6O6P / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / 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: 2.15 Å3/Da / Density % sol: 42.82 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 25% PEG 3350, 20 MM SODIUM CITRATE PROTEIN WAS CRYSTALLIZED FROM 25% PEG 3350, 20 MM SODIUM CITRATE, PH 5.5 Butyl-5'-O-adenosine phosphoramidate was soaked into the crystals using a stock ...Details: 25% PEG 3350, 20 MM SODIUM CITRATE PROTEIN WAS CRYSTALLIZED FROM 25% PEG 3350, 20 MM SODIUM CITRATE, PH 5.5 Butyl-5'-O-adenosine phosphoramidate was soaked into the crystals using a stock solution of 100 mM, to achieve ~35 mM 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 30, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3418 Å / Relative weight: 1
ReflectionResolution: 1.53→19.57 Å / Num. obs: 35060 / % possible obs: 99.5 % / Redundancy: 8.2 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 11.74
Reflection shellResolution: 1.53→1.63 Å / Redundancy: 3.88 % / Rmerge(I) obs: 0.601 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 5972 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
PROTEUM PLUSdata reduction
PROTEUM PLUSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.53→19.57 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.899 / SU B: 3.25 / SU ML: 0.112 / Cross valid method: THROUGHOUT / ESU R: 0.115 / ESU R Free: 0.12 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29675 1595 4.8 %RANDOM
Rwork0.2453 ---
obs0.24773 31580 94.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.26 Å2
Baniso -1Baniso -2Baniso -3
1--0.76 Å20 Å2-0.27 Å2
2--0.61 Å20 Å2
3---0.16 Å2
Refinement stepCycle: 1 / Resolution: 1.53→19.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1876 0 27 144 2047
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0121936
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161728
X-RAY DIFFRACTIONr_angle_refined_deg1.4891.6962617
X-RAY DIFFRACTIONr_angle_other_deg0.491.5994001
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0385241
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.74258
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.70510330
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0660.2290
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022264
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02436
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_it2.0622.37974
X-RAY DIFFRACTIONr_mcbond_other2.0362.368973
X-RAY DIFFRACTIONr_mcangle_it3.2054.2411211
X-RAY DIFFRACTIONr_mcangle_other3.2044.241212
X-RAY DIFFRACTIONr_scbond_it2.5472.642962
X-RAY DIFFRACTIONr_scbond_other2.5462.643963
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.0354.751407
X-RAY DIFFRACTIONr_long_range_B_refined6.00424.12222
X-RAY DIFFRACTIONr_long_range_B_other5.98524.042202
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.53→1.57 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.402 90 -
Rwork0.364 1884 -
obs--78.02 %

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