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- PDB-9gqp: Structural characterization of a N-acetyl-beta-neuraminic acid-bi... -

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Basic information

Entry
Database: PDB / ID: 9gqp
TitleStructural characterization of a N-acetyl-beta-neuraminic acid-binding site in human RNase2
ComponentsNon-secretory ribonuclease
KeywordsPROTEIN BINDING / Monosaccharide / Sialic acid / RNase / Immune system
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 / hydrolase 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 / hydrolase activity / Neutrophil degranulation / : / 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
ACETATE ION / N-acetyl-beta-neuraminic acid / Non-secretory ribonuclease
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.01 Å
AuthorsXincheng, K. / Jiarui, L. / Prats-Ejarque, G. / Boix, E.
Funding support Spain, 1items
OrganizationGrant numberCountry
Agencia Estatal de Investigacion (AEI)PID2022-137872NB-I00 Spain
CitationJournal: To Be Published
Title: Structural characterization of a N-acetyl-beta-neuraminic acid-binding site in human RNase2
Authors: Xincheng, K. / Jiarui, L. / Prats-Ejarque, G. / Boix, E.
History
DepositionSep 9, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 18, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Non-secretory ribonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,1907
Polymers15,6121
Non-polymers1,5786
Water4,504250
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1810 Å2
ΔGint-5 kcal/mol
Surface area8240 Å2
Unit cell
Length a, b, c (Å)41.924, 53.066, 56.457
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.) Homo sapiens (human) / Gene: RNASE2, EDN, RNS2
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P10153, pancreatic ribonuclease
#2: Sugar
ChemComp-SLB / N-acetyl-beta-neuraminic acid / N-acetylneuraminic acid / sialic acid / O-sialic acid / 5-N-ACETYL-BETA-D-NEURAMINIC ACID / BETA-SIALIC ACID


Type: D-saccharide, beta linking / Mass: 309.270 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H19NO9 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DNeup5AcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-neuraminic acidCOMMON NAMEGMML 1.0
b-D-Neup5AcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
Neu5AcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-B3P / 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL


Mass: 282.334 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H26N2O6 / Comment: pH buffer*YM
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 250 / 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: 2.07 Å3/Da / Density % sol: 40.5 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 200mM formate, 0.1M Bis-Tris propane, pH 7.0, 12% 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 9, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.01→38.67 Å / Num. obs: 54023 / % possible obs: 85.5 % / Redundancy: 5.7 % / Biso Wilson estimate: 7.96 Å2 / CC1/2: 0.998 / Net I/σ(I): 1.26
Reflection shellResolution: 1.01→1.04 Å / Num. unique obs: 607 / CC1/2: 0.922

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.01→38.67 Å / SU ML: 0.053 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 14.7984
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1507 2004 3.71 %
Rwork0.1348 52019 -
obs0.1354 54023 81.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.23 Å2
Refinement stepCycle: LAST / Resolution: 1.01→38.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1089 0 107 250 1446
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00481281
X-RAY DIFFRACTIONf_angle_d0.87451766
X-RAY DIFFRACTIONf_chiral_restr0.0742199
X-RAY DIFFRACTIONf_plane_restr0.0072229
X-RAY DIFFRACTIONf_dihedral_angle_d15.1351495
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.01-1.040.1976210.2093586X-RAY DIFFRACTION12.96
1.04-1.070.1991600.15921508X-RAY DIFFRACTION33.67
1.07-1.10.1484860.12552200X-RAY DIFFRACTION49.41
1.1-1.130.14871120.12472968X-RAY DIFFRACTION65.88
1.13-1.180.14761450.11633759X-RAY DIFFRACTION83.47
1.18-1.220.14641710.10994432X-RAY DIFFRACTION99.46
1.22-1.280.12681670.11524517X-RAY DIFFRACTION100
1.28-1.350.13771790.11724476X-RAY DIFFRACTION99.98
1.35-1.430.15211740.12394516X-RAY DIFFRACTION99.98
1.43-1.540.1431730.12154533X-RAY DIFFRACTION99.98
1.54-1.690.14631730.12744548X-RAY DIFFRACTION100
1.69-1.940.13791750.14124574X-RAY DIFFRACTION99.98
1.94-2.440.13031800.14294611X-RAY DIFFRACTION99.96
2.44-38.670.17531880.14734791X-RAY DIFFRACTION99.86

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