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- PDB-1h1h: Crystal Structure of Eosinophil Cationic Protein in Complex with ... -

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Basic information

Entry
Database: PDB / ID: 1h1h
TitleCrystal Structure of Eosinophil Cationic Protein in Complex with 2',5'-ADP at 2.0 A resolution Reveals the Details of the Ribonucleolytic Active site
ComponentsEOSINOPHIL CATIONIC PROTEIN
KeywordsHYDROLASE / EOSINOPHIL CATIONIC PROTEIN / EOSINOPHIL DERIVED NEUROTOXIN / ADENOSINE-2' / 5'-DIPHOSPHATE / RIBONUCLEASE / TOXIN
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
ADENOSINE-2'-5'-DIPHOSPHATE / Eosinophil cationic protein
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMohan, C.G. / Boix, E. / Evans, H.R. / Nikolovski, Z. / Nogues, M.V. / Cuchillo, C.M. / Acharya, K.R.
CitationJournal: Biochemistry / Year: 2002
Title: The Crystal Structure of Eosinophil Cationic Protein in Complex with 2'5'-Adp at 2.0 A Resolution Reveals the Details of the Ribonucleolytic Active Site
Authors: Mohan, C.G. / Boix, E. / Evans, H.R. / Nikolovski, Z. / Nogues, M.V. / Cuchillo, C.M. / Acharya, K.R.
History
DepositionJul 15, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 3, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 16, 2019Group: Data collection / Category: reflns_shell / Item: _reflns_shell.Rmerge_I_obs
Revision 1.4Dec 13, 2023Group: 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
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: EOSINOPHIL CATIONIC PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,1572
Polymers15,7301
Non-polymers4271
Water97354
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)100.700, 100.700, 31.700
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: Protein EOSINOPHIL CATIONIC PROTEIN / / ECP / 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) / 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-A2P / ADENOSINE-2'-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 54 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCYTOTOXIN & HELMINTHOTOXIN WITH RIBONUCLEASE ACTIVITY. MEMBER OF THE PANCREATIC RIBONUCLEASE FAMILY.

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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: 2.95 Å3/Da / Density % sol: 58.3 %
Crystal growpH: 8
Details: 0.5 M SODIUM CHLORIDE, 10% 2-PROPANOL AND 0.1 M HEPES-NAOH PH 8.0.
Crystal grow
*PLUS
Temperature: 16 ℃ / pH: 8 / Method: vapor diffusion, hanging drop
Details: microseeding, Boix, E., (1999) Biochemistry, 38, 16794.
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: PX9.6 / Wavelength: 0.8756
DetectorType: ADSC CCD / Detector: CCD / Date: Aug 15, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8756 Å / Relative weight: 1
ReflectionResolution: 2→40 Å / Num. obs: 12663 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 4.8 % / Biso Wilson estimate: 23.1 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 14.7
Reflection shellResolution: 2→2.1 Å / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 2.92 / % possible all: 99.9
Reflection
*PLUS
Highest resolution: 2 Å / Num. measured all: 61821
Reflection shell
*PLUS
% possible obs: 99.9 %

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QMT

1qmt


Resolution: 2→32.95 Å / Rfactor Rfree error: 0.008 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.21 625 5.1 %
Rwork0.205 --
obs0.205 12190 95.6 %
Displacement parametersBiso mean: 41.5 Å2
Baniso -1Baniso -2Baniso -3
1--1.13 Å20.11 Å20 Å2
2---1.13 Å20 Å2
3---2.26 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 2→32.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1101 0 27 54 1182
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
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_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.83
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
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.297 99 5.2 %
Rwork0.239 1796 -
obs--90.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
X-RAY DIFFRACTION3A2P_XPLOR_PAR.TXT
Refinement
*PLUS
Lowest resolution: 40 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.21
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.83

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