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- PDB-1qmt: Recombinant Human Eosinophil Cationic Protein -

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Basic information

Entry
Database: PDB / ID: 1qmt
TitleRecombinant Human Eosinophil Cationic Protein
ComponentsEOSINOPHIL CATIONIC PROTEIN
KeywordsRIBONUCLEASE / EOSINOPHIL / CYTOTOXICITY
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: 2.4 Å
AuthorsBoix, E. / Leonidas, D.D. / Acharya, K.R.
CitationJournal: Biochemistry / Year: 1999
Title: The Crystal Structure of Eosinophil Cationic Protein at 2.4 A Resolution
Authors: Boix, E. / Leonidas, D.D. / Nikolovski, Z. / Nogues, M.V. / Cuchillo, C.M. / Acharya, K.R.
History
DepositionOct 6, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 4, 2000Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 1, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: EOSINOPHIL CATIONIC PROTEIN


Theoretical massNumber of molelcules
Total (without water)15,7301
Polymers15,7301
Non-polymers00
Water48627
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)100.159, 100.159, 31.281
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
DetailsBIOLOGICAL_UNIT: MONOMER

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Components

#1: Protein EOSINOPHIL CATIONIC PROTEIN / / RIBONUCLEASE 3 / RNASE 3


Mass: 15730.072 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Tissue: BLOOD / Cell: EOSINOPHIL / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P12724
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 27 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSEQUENCE FOR 1QMT PDB CORRESPONDS TO RECOMBINANT HUMAN ECP. IT INCLUDES THE COMPLETE NATIVE PROTEIN ...SEQUENCE FOR 1QMT PDB CORRESPONDS TO RECOMBINANT HUMAN ECP. IT INCLUDES THE COMPLETE NATIVE PROTEIN AND AN ADDITIONAL MET AT THE N-TERMINAL. THE NATIVE ECP (RESIDUES 1 -133) CORRESPONDS TO RESIDUES 28-160 OF THE ECP PRECURSOR (SWS P12724). RESIDUES 1-27 OF P12724 ARE THE SIGNAL PEPTIDE.

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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: 3.3 Å3/Da / Density % sol: 53.2 %
Crystal growpH: 8 / Details: pH 8.00
Crystal grow
*PLUS
Temperature: 16 ℃ / Method: vapor diffusion, hanging drop / Details: microseeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
113 mg/mlprotein1drop
20.5 M1reservoirNaCl
310 %2-propanol1reservoir
40.1 MHEPES1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.5 / Wavelength: 1
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 15, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→40 Å / Num. obs: 6916 / % possible obs: 95.7 % / Observed criterion σ(I): 0 / Redundancy: 4.93 % / Biso Wilson estimate: 41.2 Å2 / Rmerge(I) obs: 0.107 / Net I/σ(I): 10.7
Reflection shellResolution: 2.4→2.49 Å / Rmerge(I) obs: 0.287 / Mean I/σ(I) obs: 3.5 / % possible all: 65
Reflection
*PLUS
Num. measured all: 34137
Reflection shell
*PLUS
% possible obs: 65 %

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Processing

Software
NameVersionClassification
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.851phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: EOSINOPHIL DERIVED NEUROTOXIN STRUCTURE AT 1.8 ANGSTROMS (COORDINATES NOT SUBMITTED) WAS PROVIDED BY S.MOSIMANN AND M.N.G.JAMES AND USED FOR MOLECULAR REPLACEMENT.

Resolution: 2.4→20 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.229 552 8 %RANDOM
Rwork0.176 ---
obs0.176 6907 95.4 %-
Displacement parametersBiso mean: 38.8 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.34 Å0.38 Å
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1102 0 0 27 1129
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.5
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d28.1
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.78
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.281.5
X-RAY DIFFRACTIONx_mcangle_it3.752
X-RAY DIFFRACTIONx_scbond_it4.152
X-RAY DIFFRACTIONx_scangle_it6.382.5
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.037 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.296 63 7.2 %
Rwork0.318 810 -
obs--74.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM.WATERTOPOW.WATER
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg28.1
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.78

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