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- PDB-1dyt: X-ray crystal structure of ECP (RNase 3) at 1.75 A -

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Basic information

Entry
Database: PDB / ID: 1dyt
TitleX-ray crystal structure of ECP (RNase 3) at 1.75 A
ComponentsEOSINOPHIL CATIONIC PROTEIN
KeywordsHYDROLASE / EOSINOPHIL CATIONIC PROTEIN / ECP / RNASE 3
Function / homology
Function and homology information


induction of bacterial agglutination / Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / RNA catabolic process / Antimicrobial peptides / RNA nuclease activity / innate immune response in mucosa / lipopolysaccharide binding / chemotaxis / antimicrobial humoral immune response mediated by antimicrobial peptide / azurophil granule lumen ...induction of bacterial agglutination / Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / RNA catabolic process / Antimicrobial peptides / RNA nuclease activity / innate immune response in mucosa / lipopolysaccharide binding / chemotaxis / antimicrobial humoral immune response mediated by antimicrobial peptide / azurophil granule lumen / antibacterial humoral response / endonuclease activity / defense response to Gram-negative bacterium / nucleic acid binding / defense response to Gram-positive bacterium / innate immune response / Neutrophil degranulation / extracellular space / 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
CITRIC ACID / : / Eosinophil cationic protein
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsMallorqui-Fernandez, G. / Pous, J. / Peracaula, R. / Maeda, T. / Tada, H. / Yamada, H. / Seno, M. / De Llorens, R. / Gomis-Rueth, F.X. / Coll, M.
CitationJournal: J.Mol.Biol. / Year: 2000
Title: Three-Dimensional Crystal Structure of Human Eosinophil Cationic Protein (Rnase 3) at 1.75 A Resolution.
Authors: Mallorqui-Fernandez, G. / Pous, J. / Peracaula, R. / Maeda, T. / Tada, H. / Yamada, H. / Seno, M. / De Llorens, R. / Gomis-Rueth, F.X. / Coll, M.
History
DepositionFeb 8, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 8, 2001Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0May 1, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _atom_site.occupancy / _database_2.pdbx_DOI ..._atom_site.occupancy / _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
Revision 2.1Nov 6, 2024Group: Advisory / Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_modification_feature ...pdbx_entry_details / pdbx_modification_feature / pdbx_struct_special_symmetry / pdbx_validate_close_contact / pdbx_validate_symm_contact

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: EOSINOPHIL CATIONIC PROTEIN
B: EOSINOPHIL CATIONIC PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0788
Polymers31,1982
Non-polymers8806
Water5,981332
1
A: EOSINOPHIL CATIONIC PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,0394
Polymers15,5991
Non-polymers4403
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: EOSINOPHIL CATIONIC PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,0394
Polymers15,5991
Non-polymers4403
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)62.163, 62.163, 174.590
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322
Components on special symmetry positions
IDModelComponents
11A-2093-

HOH

21A-2113-

HOH

31B-2046-

HOH

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Components

#1: Protein EOSINOPHIL CATIONIC PROTEIN / RIBONUCLEASE 3


Mass: 15598.876 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell: EOSINOPHIL / Gene: RNASE3 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P12724, Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Chemical
ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H8O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 332 / 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: 2.8 Å3/Da / Density % sol: 50 %
Crystal growpH: 5.2
Details: 8% JEFFAMINE M-600, 0.1M SODIUM CITRATE PH 5.2, 0.01M IRON CHLORIDE
Crystal
*PLUS
Density % sol: 50 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
111 mg/mlprotein1drop
28 %(v/v)Jeffamine M-6001reservoir
30.1 Msodium citrate1reservoir
40.01 M1reservoirFeCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1.05271
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 15, 1999 / Details: MIRRORS
RadiationMonochromator: TOROIDAL MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05271 Å / Relative weight: 1
ReflectionResolution: 1.75→22 Å / Num. obs: 35401 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 1.9 % / Rmerge(I) obs: 0.033 / Rsym value: 0.033 / Net I/σ(I): 16.3
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.03 / Mean I/σ(I) obs: 1.75 / Rsym value: 0.03 / % possible all: 99.9
Reflection
*PLUS
Num. measured all: 58607
Reflection shell
*PLUS
% possible obs: 99.9 % / Rmerge(I) obs: 0.03

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Processing

Software
NameVersionClassification
CNS0.9refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: EOSINOPHIL DERIVED PROTEIN

Resolution: 1.75→20 Å / Rfactor Rfree error: 8.0E-5 / Data cutoff high absF: 10000 / Cross valid method: MLF / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.271 3524 10 %RANDOM
Rwork0.224 ---
obs0.224 31866 91.7 %-
Solvent computationSolvent model: DENSITY MODIFICATION
Displacement parametersBiso mean: 27.403 Å2
Refinement stepCycle: LAST / Resolution: 1.75→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2188 0 54 332 2574
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.013
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_deg1.752
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
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN_REP.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER_REP.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4CIT_XPLOR_PAR.TXTCIT_XPLOR_TOP.TXT
Software
*PLUS
Name: CNS / Version: 0.9A / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS

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