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- PDB-8ub0: Structure of Histidine-5'-O-adenosine phosphoramidate/RNase A -

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Basic information

Entry
Database: PDB / ID: 8ub0
TitleStructure of Histidine-5'-O-adenosine phosphoramidate/RNase A
ComponentsRibonuclease pancreatic
KeywordsHYDROLASE / RNase-A / Nucleotide Prodrug / Amino Acidyl Phosphoramidate / Histidine-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
: / ADENOSINE MONOPHOSPHATE / DI(HYDROXYETHYL)ETHER / Ribonuclease pancreatic
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 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)28,4606
Polymers27,4172
Non-polymers1,0444
Water1,42379
1
A: Ribonuclease pancreatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2684
Polymers13,7081
Non-polymers5593
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ribonuclease pancreatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1932
Polymers13,7081
Non-polymers4841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.829, 32.807, 74.156
Angle α, β, γ (deg.)90.00, 90.18, 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 genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: RNASE1, RNS1 / Production host: Bos taurus (domestic cattle) / References: UniProt: P61823, pancreatic ribonuclease
#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-A1BA4 / (2S)-2-{[(R)-{[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl]amino}-3-(1H-imidazol-4-yl)propanoic acid (non-preferred name) / Histidine-5'-O-adenosine phosphoramidate


Mass: 484.361 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H21N8O8P / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / 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: 2.24 Å3/Da / Density % sol: 45.01 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 25% PEG 3350, 20 mM sodium citrate, pH 5.5, Histidyl-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 19, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3418 Å / Relative weight: 1
ReflectionResolution: 2→19.85 Å / Num. obs: 16652 / % possible obs: 99 % / Redundancy: 9.91 % / Rmerge(I) obs: 0.1384 / Net I/σ(I): 10.69
Reflection shellResolution: 2→2.1 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.609 / Mean I/σ(I) obs: 2.63 / Num. unique obs: 737 / % possible all: 98.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
PROTEUM PLUSdata reduction
PROTEUM PLUSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→19.85 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.876 / SU B: 8.083 / SU ML: 0.204 / Cross valid method: THROUGHOUT / ESU R: 0.259 / ESU R Free: 0.223 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.3009 903 5.5 %RANDOM
Rwork0.24203 ---
obs0.24519 15581 98.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.57 Å2
Baniso -1Baniso -2Baniso -3
1--0.65 Å20 Å2-0.52 Å2
2---0.38 Å2-0 Å2
3---1.03 Å2
Refinement stepCycle: 1 / Resolution: 2→19.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1902 0 64 79 2045
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0121987
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161769
X-RAY DIFFRACTIONr_angle_refined_deg0.9791.72684
X-RAY DIFFRACTIONr_angle_other_deg0.3561.6054097
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9085246
X-RAY DIFFRACTIONr_dihedral_angle_2_deg11.37958
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.42410336
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0470.2296
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022331
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02451
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_it3.7443.622993
X-RAY DIFFRACTIONr_mcbond_other3.7433.628994
X-RAY DIFFRACTIONr_mcangle_it5.8456.4781236
X-RAY DIFFRACTIONr_mcangle_other5.8346.4751236
X-RAY DIFFRACTIONr_scbond_it4.013.998994
X-RAY DIFFRACTIONr_scbond_other4.0083.999995
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.2967.1951449
X-RAY DIFFRACTIONr_long_range_B_refined9.65135.982234
X-RAY DIFFRACTIONr_long_range_B_other9.65935.822218
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.387 84 -
Rwork0.334 1145 -
obs--98.24 %

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