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- PDB-1gqv: Atomic Resolution (0.98A) Structure of Eosinophil-Derived Neurotoxin -

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Basic information

Entry
Database: PDB / ID: 1gqv
TitleAtomic Resolution (0.98A) Structure of Eosinophil-Derived Neurotoxin
ComponentsEOSINOPHIL-DERIVED NEUROTOXIN
KeywordsRNASE-2 / RNASE US / RIBONUCLEASE
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
P-30 Protein / Ribonuclease A-like domain / Pancreatic ribonuclease / Ribonuclease A, active site / Ribonuclease A-domain / Ribonuclease A-like domain superfamily / Pancreatic ribonuclease / Pancreatic ribonuclease family signature. / Pancreatic ribonuclease / Roll / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Non-secretory ribonuclease
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.98 Å
AuthorsSwaminathan, G.J. / Holloway, D.E. / Veluraja, K. / Acharya, K.R.
Citation
Journal: Biochemistry / Year: 2002
Title: Atomic Resolution (0.98 A) Structure of Eosinophil-Derived Neurotoxin
Authors: Swaminathan, G.J. / Holloway, D.E. / Veluraja, K. / Acharya, K.R.
#1: Journal: J.Biol.Chem. / Year: 2001
Title: Mapping the Ribonucleolytic Active Site of Eosinophil-Derived Neurotoxin (Edn): High Resolution Crystal Structures of Edn Complexes with Adenylic Nucleotide Inhibitors
Authors: Leonidas, D.D. / Boix, E. / Prill, R. / Suzuki, M. / Turton, R. / Minson, K. / Swaminathan, G.J. / Youle, R.J. / Acharya, K.R.
History
DepositionDec 5, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 8, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 22, 2019Group: Data collection / Other / Refinement description
Category: pdbx_database_proc / pdbx_database_status / refine
Item: _pdbx_database_status.recvd_author_approval / _refine.pdbx_ls_cross_valid_method
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: EOSINOPHIL-DERIVED NEUROTOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6712
Polymers15,6121
Non-polymers591
Water4,071226
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)53.024, 57.477, 42.398
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein EOSINOPHIL-DERIVED NEUROTOXIN / RNASE-2 / RNASE-US / EDN


Mass: 15611.750 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Tissue: BLOOD / Cell: EOSINOPHIL / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P10153, EC: 3.1.27.5
#2: Chemical ChemComp-ACT / ACETATE ION


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


Mass: 18.015 Da / Num. of mol.: 226 / Source method: isolated from a natural source / Formula: H2O
Compound detailsN-TERMINAL MET IS AN EXPRESSION SYSTEM ARTEFACT

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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: 1.79 Å3/Da / Density % sol: 36.85 %
Crystal growpH: 6.5 / Details: 1.4M SODIUM ACETATE, 0.1M MES PH 6.5
Crystal grow
*PLUS
Temperature: 16 ℃ / Method: vapor diffusion, hanging drop / pH: 6.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
11.7 mg/mlprotein1drop
20.05 Msodium cacodylate1droppH6.5
30.7 Msodium acetate1drop
40.1 Msodium cacodylate1reservoirpH6.5
51.4 Msodium acetate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: ADSC CCD / Detector: CCD / Date: Mar 20, 2001
RadiationMonochromator: DARESBURY / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 0.98→40 Å / Num. obs: 74763 / % possible obs: 99.6 % / Redundancy: 8.18 % / Rsym value: 0.057 / Net I/σ(I): 21.67
Reflection shellResolution: 0.98→1.02 Å / Redundancy: 6.5 % / Mean I/σ(I) obs: 3.7 / Rsym value: 0.42 / % possible all: 99.9
Reflection
*PLUS
Num. measured all: 614353 / Rmerge(I) obs: 0.057
Reflection shell
*PLUS
Highest resolution: 0.98 Å / Lowest resolution: 1.02 Å / % possible obs: 99.9 % / Rmerge(I) obs: 0.421

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Processing

Software
NameVersionClassification
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1phasing
SHELXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HI2

1hi2


Resolution: 0.98→10 Å / Num. parameters: 12576 / Num. restraintsaints: 15543 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY ?
RfactorNum. reflection% reflectionSelection details
Rfree0.1444 1031 1.35 %RANDOM
all0.1159 74606 --
obs0.116 -98.2 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-2
Refine analyzeNum. disordered residues: 17 / Occupancy sum hydrogen: 1029 / Occupancy sum non hydrogen: 1279.5
Refinement stepCycle: LAST / Resolution: 0.98→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1088 0 4 226 1318
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.012
X-RAY DIFFRACTIONs_angle_d0.034
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0339
X-RAY DIFFRACTIONs_zero_chiral_vol0.158
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.163
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.119
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.019
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.024
X-RAY DIFFRACTIONs_approx_iso_adps0.086
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
% reflection Rfree: 1.5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal targetDev ideal
X-RAY DIFFRACTIONs_bond_d0.03
X-RAY DIFFRACTIONs_angle_d0.06
X-RAY DIFFRACTIONs_plane_restr0.0339
X-RAY DIFFRACTIONs_chiral_restr0.158

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