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- PDB-8qew: Eosinophil Derived Neurotoxin/RNase 2 in complex with Tartrate -

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Basic information

Entry
Database: PDB / ID: 8qew
TitleEosinophil Derived Neurotoxin/RNase 2 in complex with Tartrate
ComponentsNon-secretory ribonuclease
KeywordsIMMUNE SYSTEM / anion binding site / RNase
Function / homology
Function and homology information


RNA catabolic process / pancreatic ribonuclease / ribonuclease A activity / RNA nuclease activity / innate immune response in mucosa / chemotaxis / azurophil granule lumen / defense response to virus / nucleic acid binding / lyase activity ...RNA catabolic process / pancreatic ribonuclease / ribonuclease A activity / RNA nuclease activity / innate immune response in mucosa / chemotaxis / azurophil granule lumen / defense response to virus / nucleic acid binding / lyase activity / Neutrophil degranulation / extracellular space / extracellular exosome / 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
L(+)-TARTARIC ACID / Non-secretory ribonuclease
Similarity search - Component
Biological speciesEscherichia coli 'BL21-GoldpLysS AG'
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsLi, J. / Kang, X. / Prats-Ejarque, G. / Boix, E.
Funding support Spain, 1items
OrganizationGrant numberCountry
Agencia Estatal de Investigacion (AEI)PID2019-106123GB-I00 Spain
CitationJournal: To Be Published
Title: Eosinophil Derived Neurotoxin/RNase 2 in complex with Tartrate
Authors: Li, J. / Kang, X. / Prats-Ejarque, G. / Boix, E.
History
DepositionSep 1, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 11, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 16, 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

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Assembly

Deposited unit
A: Non-secretory ribonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,0624
Polymers15,6121
Non-polymers4503
Water2,774154
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area910 Å2
ΔGint1 kcal/mol
Surface area7410 Å2
Unit cell
Length a, b, c (Å)41.793, 52.677, 56.421
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Non-secretory ribonuclease / Eosinophil-derived neurotoxin / RNase UpI-2 / Ribonuclease 2 / RNase 2 / Ribonuclease US


Mass: 15611.750 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Gene: RNASE2, EDN, RNS2
Production host: Cloning vector pET-T7p(-14G)-SpacerA-GFP-LVA (others)
References: UniProt: P10153, pancreatic ribonuclease
#2: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H6O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / 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: 1.99 Å3/Da / Density % sol: 38.16 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Ammonium tartrate dibasic pH 7.0, 20% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 15, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.197→38.5 Å / Num. obs: 34213 / % possible obs: 89.4 % / Redundancy: 5.2 % / Biso Wilson estimate: 8.49 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 13.9
Reflection shellResolution: 1.197→1.252 Å / Rmerge(I) obs: 0.35 / Num. unique obs: 1711

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.2→38.5 Å / SU ML: 0.1039 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 20.0336
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1932 1991 5.82 %
Rwork0.1738 32220 -
obs0.175 34211 85.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 12.36 Å2
Refinement stepCycle: LAST / Resolution: 1.2→38.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1088 0 30 154 1272
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00541178
X-RAY DIFFRACTIONf_angle_d0.90661618
X-RAY DIFFRACTIONf_chiral_restr0.0809179
X-RAY DIFFRACTIONf_plane_restr0.0101220
X-RAY DIFFRACTIONf_dihedral_angle_d6.1495158
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2-1.230.3803480.2795703X-RAY DIFFRACTION26.64
1.23-1.260.2576710.25071206X-RAY DIFFRACTION45.74
1.26-1.30.20351060.22151664X-RAY DIFFRACTION63.21
1.3-1.340.22561260.20692052X-RAY DIFFRACTION77.12
1.34-1.390.22851400.19422351X-RAY DIFFRACTION88.24
1.39-1.440.17671610.17642556X-RAY DIFFRACTION95.84
1.44-1.510.21011620.17452642X-RAY DIFFRACTION99.86
1.51-1.590.17131640.16732663X-RAY DIFFRACTION99.96
1.59-1.690.18481660.17252699X-RAY DIFFRACTION99.97
1.69-1.820.20231710.17762680X-RAY DIFFRACTION99.93
1.82-20.20761580.17152705X-RAY DIFFRACTION99.93
2-2.290.18471750.16662688X-RAY DIFFRACTION99.83
2.29-2.880.18481650.17812746X-RAY DIFFRACTION99.79
2.88-38.50.18121780.15662865X-RAY DIFFRACTION99.57
Refinement TLS params.Method: refined / Origin x: -10.2949238357 Å / Origin y: 9.11155689706 Å / Origin z: -10.0750036173 Å
111213212223313233
T0.0405085585833 Å20.00141816837938 Å2-0.00289693157996 Å2-0.0580101204127 Å20.013307599944 Å2--0.0430134015673 Å2
L0.753428963616 °2-0.22683306449 °2-0.424167003684 °2-1.23806754582 °20.759314461543 °2--1.03736951949 °2
S0.0200117649608 Å °0.0367510352406 Å °0.0353741311216 Å °-0.0423683975577 Å °-0.0139584706715 Å °0.0278884136298 Å °-0.0170488895347 Å °-0.0274787987033 Å °-0.000959250755293 Å °
Refinement TLS groupSelection details: all

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