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- PDB-5f3p: Crystal structure of a noncanonical Dicer protein from Entamoeba ... -

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Basic information

Entry
Database: PDB / ID: 5f3p
TitleCrystal structure of a noncanonical Dicer protein from Entamoeba histolytica
ComponentsPutative uncharacterized protein
KeywordsRNA BINDING PROTEIN / RNaseIII / non canonical Dicer / RNA procesing / Entamoeba histolytica
Function / homologyribonuclease III activity / Ribonuclease III, endonuclease domain superfamily / RNA processing / metal ion binding / Uncharacterized protein
Function and homology information
Biological speciesEntamoeba histolytica (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.904 Å
AuthorsYu, X. / Gan, J.H. / Ma, J.B.
CitationJournal: To Be Published
Title: Structural and functional study of a noncanonical Dicer protein in Entamoeba histolytica
Authors: Yu, X. / Gan, J.H. / Ma, J.B.
History
DepositionDec 3, 2015Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 8, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative uncharacterized protein
B: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,9804
Polymers45,7882
Non-polymers1922
Water1,36976
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2640 Å2
ΔGint-37 kcal/mol
Surface area17910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.092, 89.956, 100.358
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Putative uncharacterized protein / EhRNaseIII


Mass: 22893.994 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 2-195
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Entamoeba histolytica (eukaryote) / Gene: EHI_068740 / Production host: Escherichia coli (E. coli) / References: UniProt: C4LU64
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / Source method: isolated from a natural source / Formula: H2O

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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: 2.28 Å3/Da / Density % sol: 46.05 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 1.6 M (NH4)2SO4, 0.01 M MgCl2, 0.05 M Tris-HCl pH 7.5
PH range: 7.4-7.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 18, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. obs: 31630 / % possible obs: 94.8 % / Redundancy: 6.6 % / Net I/σ(I): 26.8

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155)refinement
HKL-2000data processing
Cootv0.8.3model building
RefinementResolution: 1.904→28.73 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2398 1592 5.05 %
Rwork0.2073 --
obs0.209 31554 94.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.904→28.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3148 0 10 76 3234
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083228
X-RAY DIFFRACTIONf_angle_d0.8044357
X-RAY DIFFRACTIONf_dihedral_angle_d15.4811916
X-RAY DIFFRACTIONf_chiral_restr0.042473
X-RAY DIFFRACTIONf_plane_restr0.005546
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9036-1.9650.54491460.53582620X-RAY DIFFRACTION93
1.965-2.03520.24831530.24122846X-RAY DIFFRACTION100
2.0352-2.11670.21881520.18192832X-RAY DIFFRACTION100
2.1167-2.2130.19291490.16522862X-RAY DIFFRACTION100
2.213-2.32960.3392950.22991853X-RAY DIFFRACTION65
2.3296-2.47550.18711470.17582876X-RAY DIFFRACTION100
2.4755-2.66650.25951430.18312875X-RAY DIFFRACTION100
2.6665-2.93460.23861480.19522894X-RAY DIFFRACTION100
2.9346-3.35870.23931580.1982907X-RAY DIFFRACTION100
3.3587-4.22940.18891300.18442476X-RAY DIFFRACTION84
4.2294-28.73360.22581710.19172921X-RAY DIFFRACTION96

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