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- PDB-4oxf: Structure of ECP in complex with citrate ions at 1.50 Angstroms -

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Basic information

Entry
Database: PDB / ID: 4oxf
TitleStructure of ECP in complex with citrate ions 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 / 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 / Resolution: 1.5 Å
AuthorsBlanco, J.A. / Boix, E. / Moussaoui, M. / Salazar, V.A.
Funding support Spain, 1items
OrganizationGrant numberCountry
Ministerio de Economia y CompetitividadBFU2012-38965 Spain
Citation
Journal: To be published
Title: Structure of ECP in complex with citrate ions at 1.50 Angstroms
Authors: Blanco, J.A. / Boix, E. / Moussaoui, M. / Salazar, V.A.
#1: Journal: 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. / Aymami, J. / Maeda, T. / Tada, H. / Yamada, H. / Seno, M. / de Llorens, R. / Gomis-Ruth, F.X. / Coll, M.
#2: 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: Advisory / Data collection ...Advisory / 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_conn_angle / pdbx_struct_oper_list / pdbx_validate_close_contact / pdbx_validate_symm_contact / refine_hist / struct_conn / 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_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry / _struct_keywords.text / _struct_site.details / _symmetry.Int_Tables_number
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)32,5329
Polymers31,4602
Non-polymers1,0727
Water7,206400
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)65,06518
Polymers62,9204
Non-polymers2,14514
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_455-x-1,y,-z1
MethodPISA
Unit cell
Length a, b, c (Å)62.535, 62.535, 175.050
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322

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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-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 400 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsAUTHORS STATE THAT BOTH IRON AND CITRATE ATOMS HAVE BEEN ADJUSTED TO THE CORRESPONDING ELECTRON ...AUTHORS STATE THAT BOTH IRON AND CITRATE ATOMS HAVE BEEN ADJUSTED TO THE CORRESPONDING ELECTRON DENSITY. CIT302 SURROUNDS THE SAME-CHAIN IRON ATOM, WHICH CAN ALSO COORDINATE SOME SURROUNDING WATER MOLECULES. THESE HAVE BEEN DIFFICULT TO ADJUST AS THE ELECTRON DENSITY AROUND THE IRON ATOMS IS NOT SPHERICAL AND THE WATER MOLECULES THERE WOULD NOT HAVE A DEFINED FIXED POSITION. THE SURROUNDING CITRATE LIGAND ALSO SHOWED HIGH MOBILITY. THESE PROBLEMS ALTOGETHER MAKE REFINEMENT STEPS MOVE THE CITRATE LIGAND IN SUCH A POSITION THAT CLASHES APPEARED.

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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: 2.73 Å3/Da / Density % sol: 54.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.2
Details: Protein resuspended in sodium cacodylate buffer (20mM, pH5.0). 1 uL of protein sample was mixed with 1 uL of crystallisation buffer (0.1M sodium citrate pH5.2, 8% Jeffamine M-600, 10mM iron(III) chloride)
PH range: 5.0 - 5.2

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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→52.53 Å / Num. obs: 61922 / % possible obs: 99.3 % / Redundancy: 8.6 % / Rmerge(I) obs: 0.03 / Net I/σ(I): 32.3
Reflection shellResolution: 1.5→1.62 Å / Mean I/σ(I) obs: 3.8 / % possible all: 100

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.4_1496) / Classification: refinement
RefinementResolution: 1.5→50.882 Å / SU ML: 0.15 / σ(F): 1.35 / Phase error: 22.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2314 2834 5.06 %
Rwork0.1969 --
obs0.1986 55982 98.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.5→50.882 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2196 0 67 400 2663
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072465
X-RAY DIFFRACTIONf_angle_d1.1493354
X-RAY DIFFRACTIONf_dihedral_angle_d18.228970
X-RAY DIFFRACTIONf_chiral_restr0.049356
X-RAY DIFFRACTIONf_plane_restr0.006451
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.52590.27481270.2572667X-RAY DIFFRACTION100
1.5259-1.55360.31871510.25242592X-RAY DIFFRACTION100
1.5536-1.58350.28621250.24592647X-RAY DIFFRACTION100
1.5835-1.61580.26691620.24312620X-RAY DIFFRACTION100
1.6158-1.6510.25611550.22832636X-RAY DIFFRACTION100
1.651-1.68940.22581350.22562657X-RAY DIFFRACTION100
1.6894-1.73160.2431440.22332630X-RAY DIFFRACTION100
1.7316-1.77840.24411420.22812644X-RAY DIFFRACTION100
1.7784-1.83080.27181270.22762653X-RAY DIFFRACTION100
1.8308-1.88990.23631450.21532651X-RAY DIFFRACTION100
1.8899-1.95740.2351320.21012678X-RAY DIFFRACTION99
1.9574-2.03580.25961590.2112600X-RAY DIFFRACTION99
2.0358-2.12840.2451430.20322657X-RAY DIFFRACTION99
2.1284-2.24070.24341470.20912670X-RAY DIFFRACTION99
2.2407-2.3810.25481290.19982654X-RAY DIFFRACTION99
2.381-2.56490.27421410.19912646X-RAY DIFFRACTION98
2.5649-2.8230.23931510.20142660X-RAY DIFFRACTION98
2.823-3.23140.22261350.19322685X-RAY DIFFRACTION98
3.2314-4.0710.16731440.15952688X-RAY DIFFRACTION96
4.071-50.91140.22761400.18362813X-RAY DIFFRACTION94

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