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- PDB-4x08: Structure of H128N/ECP mutant in complex with sulphate anions at ... -

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Basic information

Entry
Database: PDB / ID: 4x08
TitleStructure of H128N/ECP mutant in complex with sulphate anions at 1.34 Angstroms.
ComponentsEosinophil cationic protein
KeywordsHYDROLASE / active centre mutation / sulphate / sulphate recognition site / 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
Eosinophil cationic protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.34 Å
AuthorsBlanco, J.A. / Garcia, J.M. / Salazar, V.A. / Sanchez, D. / Moussauoi, M. / Boix, E.
Citation
Journal: To Be Published
Title: Structure of H128N/ECP mutant in complex with sulphate anions at 1.34 Angstroms.
Authors: Blanco, J.A. / Garcia, J.M. / Salazar, V.A. / Sanchez, D. / Moussauoi, M. / Boix, E.
#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.
#2: 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.
History
DepositionNov 21, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 7, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: 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 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)32,94918
Polymers31,4122
Non-polymers1,53716
Water7,602422
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3720 Å2
ΔGint-170 kcal/mol
Surface area15690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.867, 51.104, 55.601
Angle α, β, γ (deg.)90.00, 111.09, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-204-

SO4

21A-395-

HOH

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Components

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


Mass: 15706.027 Da / Num. of mol.: 2 / Mutation: H128N
Source method: isolated from a genetically manipulated source
Details: Residue 97 corresponds to a protein natural variant
Source: (gene. exp.) Homo sapiens (human) / Cell: EOSINOPHILS / Gene: RNASE3, ECP, RNS3 / Organ: BONE MARROW / Plasmid: pET11 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P12724, Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters, EC: 3.1.27.5
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 16
Source method: isolated from a genetically manipulated source
Formula: SO4 / Source: (gene. exp.) Homo sapiens (human) / Gene: RNASE3, ECP, RNS3 / Plasmid: pET11 / Production host: Escherichia coli BL21(DE3) (bacteria)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 422 / 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

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Sample preparation

CrystalDensity Matthews: 1.98 Å3/Da / Density % sol: 38.01 % / Description: NEEDLE-SHAPED CRYSTALS
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: CRYSTALS GREW FROM A CRYSTALLISATION CONDITION BASED ON 0.2M LITHIUM SULPHATE, 0.1M TRIS BUFFER, pH8.5 AND 15% PEG4000

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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: Oct 24, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.34→41.37 Å / Num. all: 54033 / Num. obs: 54033 / % possible obs: 98.8 % / Redundancy: 1.82 % / Rmerge(I) obs: 0.038 / Net I/σ(I): 10.9
Reflection shellResolution: 1.34→1.39 Å / Rmerge(I) obs: 0.371 / Mean I/σ(I) obs: 2.1 / % possible all: 97.9

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
XDSdata reduction
Cootmodel building
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4A2O

4a2o


Resolution: 1.34→41.37 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2179 2629 4.87 %
Rwork0.1838 --
obs0.1855 54029 98.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.34→41.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2192 0 80 422 2694
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072474
X-RAY DIFFRACTIONf_angle_d1.0543379
X-RAY DIFFRACTIONf_dihedral_angle_d12.362938
X-RAY DIFFRACTIONf_chiral_restr0.049357
X-RAY DIFFRACTIONf_plane_restr0.006439
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3396-1.3640.28681560.27622595X-RAY DIFFRACTION97
1.364-1.39020.30221310.26122740X-RAY DIFFRACTION99
1.3902-1.41860.27121210.23962679X-RAY DIFFRACTION99
1.4186-1.44940.27941500.22812665X-RAY DIFFRACTION99
1.4494-1.48320.25511180.22252720X-RAY DIFFRACTION99
1.4832-1.52020.26781350.20892706X-RAY DIFFRACTION99
1.5202-1.56140.24881210.20572722X-RAY DIFFRACTION99
1.5614-1.60730.22891220.20542718X-RAY DIFFRACTION99
1.6073-1.65920.24021430.19772726X-RAY DIFFRACTION99
1.6592-1.71850.2261530.19292701X-RAY DIFFRACTION99
1.7185-1.78730.22671530.19492669X-RAY DIFFRACTION100
1.7873-1.86860.21761360.18792736X-RAY DIFFRACTION99
1.8686-1.96710.22761330.18052699X-RAY DIFFRACTION99
1.9671-2.09040.2081300.17162723X-RAY DIFFRACTION99
2.0904-2.25180.20741530.17462693X-RAY DIFFRACTION99
2.2518-2.47840.20461500.17642693X-RAY DIFFRACTION99
2.4784-2.83690.21681280.18342723X-RAY DIFFRACTION98
2.8369-3.57390.21141600.16532719X-RAY DIFFRACTION99
3.5739-41.39330.18321360.16172773X-RAY DIFFRACTION98

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