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- PDB-6xhe: Structure of beta-prolinyl 5'-O-adenosine phosphoramidate -

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Basic information

Entry
Database: PDB / ID: 6xhe
TitleStructure of beta-prolinyl 5'-O-adenosine phosphoramidate
ComponentsRibonuclease pancreatic
KeywordsRNA BINDING PROTEIN / RNase A complex / phosphoramidate structure
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 / Chem-V2J / Ribonuclease pancreatic
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsPallan, P.S. / Egli, M.
Funding support Germany, 1items
OrganizationGrant numberCountry
Volkswagen Foundationgrant Az 92 768 Germany
CitationJournal: 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
DepositionJun 18, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 17, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)28,2084
Polymers27,4172
Non-polymers7922
Water1,76598
1
A: Ribonuclease pancreatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0562
Polymers13,7081
Non-polymers3471
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ribonuclease pancreatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1532
Polymers13,7081
Non-polymers4441
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)101.002, 32.795, 74.090
Angle α, β, γ (deg.)90.00, 90.33, 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 / Organ: Pancreas / Organ (production host): Pancreas / 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-V2J / 5'-O-[(S)-[(3S)-3-carboxypyrrolidin-1-yl](hydroxy)phosphoryl]adenosine


Mass: 444.336 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H21N6O8P / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / 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: 45.03 %
Crystal growTemperature: 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-5'-O-adenosine phosphoramidate soaking was achieved as follows. 1 uL of a stock solution of 50 mM ligand ...Details: PROTEIN WAS CRYSTALLIZED FROM 25% PEG 3350, 20 MM SODIUM CITRATE, PH 5.5, Glycinyl-5'-O-adenosine phosphoramidate soaking was achieved as follows. 1 uL of a stock solution of 50 mM ligand was added to 2uL of reservoir solution, to achieve a concentration of ~25 mM in the soaking solution. A few RNase A crystals were soaked for 45 - 90 minutes in the soaking solution

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jul 10, 2019 / Details: C(111)
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.88→29.81 Å / Num. obs: 19587 / % possible obs: 98.2 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.094 / Rsym value: 0.094 / Net I/σ(I): 24.93
Reflection shellResolution: 1.88→1.97 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.951 / Num. unique obs: 1765 / Rsym value: 0.951 / % possible all: 89.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Single RNase molecule from PDB-ID

Resolution: 1.88→29.81 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.932 / SU B: 6.451 / SU ML: 0.173 / Cross valid method: THROUGHOUT / ESU R: 0.176 / ESU R Free: 0.17 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26463 968 4.9 %RANDOM
Rwork0.20482 ---
obs0.20769 18618 96.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.318 Å2
Baniso -1Baniso -2Baniso -3
1--1.83 Å2-0 Å2-1.67 Å2
2---2.12 Å20 Å2
3---3.96 Å2
Refinement stepCycle: 1 / Resolution: 1.88→29.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1902 0 53 98 2053
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0132000
X-RAY DIFFRACTIONr_bond_other_d0.0010.0181697
X-RAY DIFFRACTIONr_angle_refined_deg1.5781.6812716
X-RAY DIFFRACTIONr_angle_other_deg1.3191.5953992
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1015246
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.04323.95896
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.04415336
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.406158
X-RAY DIFFRACTIONr_chiral_restr0.0610.2278
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022228
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02376
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_it3.2374.544992
X-RAY DIFFRACTIONr_mcbond_other3.2284.536989
X-RAY DIFFRACTIONr_mcangle_it4.9376.8021235
X-RAY DIFFRACTIONr_mcangle_other4.9376.7961235
X-RAY DIFFRACTIONr_scbond_it3.6064.9181006
X-RAY DIFFRACTIONr_scbond_other3.6054.9181007
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.3457.2531482
X-RAY DIFFRACTIONr_long_range_B_refined8.5854.3032193
X-RAY DIFFRACTIONr_long_range_B_other8.56454.2982184
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.88→1.929 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.323 67 -
Rwork0.348 1069 -
obs--75.13 %

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