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- PDB-2c01: Crystal Structures of Eosinophil-derived Neurotoxin in Complex wi... -

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Basic information

Entry
Database: PDB / ID: 2c01
TitleCrystal Structures of Eosinophil-derived Neurotoxin in Complex with the Inhibitors 5'-ATP, Ap3A, Ap4A and Ap5A
ComponentsNONSECRETORY RIBONUCLEASE
KeywordsHYDROLASE / ENDONUCLEASE / EOSINOPHIL / NUCLEASE / RIBONUCLEASE / RNASE US / RNASE-2 / INHIBITOR / 5'-ATP / AP3A / AP4A / AP5A / CHEMOTAXIS / GLYCOPROTEIN / POLYMORPHISM / SENSORY TRANSDUCTION
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
ACETIC ACID / ADENOSINE-5'-TRIPHOSPHATE / Non-secretory ribonuclease
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.24 Å
AuthorsBaker, M.D. / Holloway, D.E. / Swaminathan, G.J. / Acharya, K.R.
CitationJournal: Biochemistry / Year: 2006
Title: Crystal Structures of Eosinophil-Derived Neurotoxin (Edn) in Complex with the Inhibitors 5'- ATP, Ap(3)A, Ap(4)A, and Ap(5)A.
Authors: Baker, M.D. / Holloway, D.E. / Swaminathan, G.J. / Acharya, K.R.
History
DepositionAug 24, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 18, 2006Provider: repository / Type: Initial release
Revision 1.1Jun 2, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 11, 2020Group: Derived calculations / Other
Category: pdbx_database_status / struct_conn / struct_conn_type
Item: _pdbx_database_status.status_code_sf
Revision 1.4Dec 13, 2023Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
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

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Assembly

Deposited unit
X: NONSECRETORY RIBONUCLEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,1793
Polymers15,6121
Non-polymers5672
Water4,288238
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)52.700, 56.710, 41.970
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 NONSECRETORY RIBONUCLEASE / EOSINOPHIL-DERIVED NEUROTOXIN / RIBONUCLEASE US / RNASE UPI-2 / RIBONUCLEASE 2 / RNASE 2


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


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 238 / Source method: isolated from a natural source / Formula: H2O
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: 1.63 Å3/Da / Density % sol: 24.07 %
Crystal growpH: 6.5 / Details: pH 6.50

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Data collection

DiffractionMean temperature: 203 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.979
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.24→40 Å / Num. obs: 36418 / % possible obs: 99.1 % / Observed criterion σ(I): 2 / Redundancy: 10.07 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 32.1
Reflection shellResolution: 1.24→1.28 Å / Rmerge(I) obs: 0.13 / Mean I/σ(I) obs: 13.7 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GQV

1gqv


Resolution: 1.24→40 Å / Cross valid method: THROUGHOUT / σ(F): 2
Details: GAMMA PHOSPHATE OF ATP NOT MODELLED DUE TO POOR DENSITY. ALPHA AND BETA PHOSPHATES MODELLED IN TWO ALTERNATE CONFROMATIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.221 -4 %RANDOM
Rwork0.188 ---
obs0.188 366963 99.1 %-
Refinement stepCycle: LAST / Resolution: 1.24→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1088 0 33 238 1359
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.36
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it

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