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- PDB-4oxb: Structure of ECP with sulphate anions at 1.50 Angstroms -

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Basic information

Entry
Database: PDB / ID: 4oxb
TitleStructure of ECP with sulphate anions at 1.50 Angstroms
ComponentsEosinophil cationic protein
KeywordsHYDROLASE / RNase 3 / Eosinophil Cationic Protein (ECP)
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 / azurophil granule lumen / antimicrobial humoral immune response mediated by antimicrobial peptide ...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 / azurophil granule lumen / antimicrobial humoral immune response mediated by antimicrobial peptide / antibacterial humoral response / endonuclease activity / nucleic acid binding / defense response to Gram-negative bacterium / 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
Eosinophil cationic protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.5 Å
AuthorsBlanco, J.A. / Boix, E. / Moussaoui, M.
Funding support Spain, 1items
OrganizationGrant numberCountry
Ministerio de Economia y CompetitividadBFU2012-38965 Spain
Citation
Journal: To be published
Title: Structure of ECP at 1.50 with sulphate anions at 1.50 Angstroms
Authors: Blanco, J.A. / Boix, E. / Moussaoui, M.
#1: Journal: J.Struct.Biol. / Year: 2012
Title: The sulfate-binding site structure of the human eosinophil cationic protein as revealed by a new crystal form.
Authors: Boix, E. / Pulido, D. / Moussaoui, M. / Nogues, M.V. / Russi, S.
History
DepositionFeb 5, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / entity_src_gen / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / refine_hist / struct_keywords / struct_site / symmetry
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text / _struct_site.details / _symmetry.Int_Tables_number
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)32,70915
Polymers31,4602
Non-polymers1,24913
Water6,684371
1
A: Eosinophil cationic protein
B: Eosinophil cationic protein
hetero molecules

A: Eosinophil cationic protein
B: Eosinophil cationic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,41830
Polymers62,9204
Non-polymers2,49826
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area7990 Å2
ΔGint-309 kcal/mol
Surface area29380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.730, 51.286, 55.619
Angle α, β, γ (deg.)90.00, 111.25, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Eosinophil cationic protein / ECP / Ribonuclease 3 / RNase 3


Mass: 15730.072 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue: Bone marrow / Cell: Eosinophil / Gene: ECP,RNASE3,RNS3 / Plasmid: pET11c / Cell (production host): Bacteria / 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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 371 / 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: 1.96 Å3/Da / Density % sol: 37.21 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: Protein resuspended in 20mM sodium cacodylate buffer, pH5.0. 1 uL of protein sample mixed with 1 uL of crystallisation buffer (0.2M lithium sulphate, 0.1M TRIS-HCl pH8.5, 15% PEG4000).
PH range: 5.0 - 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 10, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.5→44.12 Å / Num. obs: 38779 / % possible obs: 99.3 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 8.3
Reflection shellResolution: 1.5→1.58 Å / Rmerge(I) obs: 0.497 / Mean I/σ(I) obs: 2.4 / % possible all: 99.3

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.4_1496) / Classification: refinement
RefinementResolution: 1.5→44.105 Å / SU ML: 0.18 / σ(F): 1.34 / Phase error: 23.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2315 1938 5.01 %
Rwork0.1792 --
obs0.1818 38665 98.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.5→44.105 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2188 0 65 371 2624
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072452
X-RAY DIFFRACTIONf_angle_d1.0143339
X-RAY DIFFRACTIONf_dihedral_angle_d13.24939
X-RAY DIFFRACTIONf_chiral_restr0.043355
X-RAY DIFFRACTIONf_plane_restr0.006433
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.53750.29481280.22382638X-RAY DIFFRACTION100
1.5375-1.57910.26981490.21942626X-RAY DIFFRACTION100
1.5791-1.62560.25631280.19792622X-RAY DIFFRACTION99
1.6256-1.6780.24941270.20112655X-RAY DIFFRACTION100
1.678-1.7380.26041360.2062612X-RAY DIFFRACTION99
1.738-1.80760.24741370.20032632X-RAY DIFFRACTION99
1.8076-1.88990.22531430.20442622X-RAY DIFFRACTION99
1.8899-1.98950.2871620.20072548X-RAY DIFFRACTION98
1.9895-2.11410.24461190.18242641X-RAY DIFFRACTION99
2.1141-2.27740.24391400.18442519X-RAY DIFFRACTION95
2.2774-2.50650.21061440.17162614X-RAY DIFFRACTION99
2.5065-2.86920.25121510.17832632X-RAY DIFFRACTION99
2.8692-3.61460.22941470.1592648X-RAY DIFFRACTION99
3.6146-44.12430.18311270.16382718X-RAY DIFFRACTION99

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