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- PDB-5f3q: Crystal structure of a noncanonical Dicer protein from Entamoeba ... -

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Basic information

Entry
Database: PDB / ID: 5f3q
TitleCrystal structure of a noncanonical Dicer protein from Entamoeba histolytica
ComponentsPutative uncharacterized protein
KeywordsRNA BINDING PROTEIN / RNaseIII / Dicer / RNA processing / 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 / SAD / Resolution: 2.1 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: RCSB / Processing site: PDBJ
Revision 1.0Dec 14, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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)45,7494
Polymers45,5572
Non-polymers1922
Water1,33374
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2450 Å2
ΔGint-36 kcal/mol
Surface area16830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.281, 91.015, 102.746
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 / Eh.RNaseIII


Mass: 22778.357 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 2-193
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.: 74 / 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: 2.24 Å3/Da / Density % sol: 45.12 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: 1.26 M (NH4)2SO4, 0.1 M Hepes pH 7.8 / PH range: 7.5-7.9

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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: Oct 15, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. obs: 24145 / % possible obs: 99.1 % / Redundancy: 3.8 % / Net I/σ(I): 24.2
Reflection shellResolution: 2.1→2.18 Å

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Processing

Software
NameVersionClassification
HKL-2000data processing
Cootmodel building
PHENIX(1.10_2155)refinement
RefinementMethod to determine structure: SAD / Resolution: 2.1→29.996 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2464 1230 5.09 %
Rwork0.2016 --
obs0.2039 24145 98.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→29.996 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2981 0 10 74 3065
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073056
X-RAY DIFFRACTIONf_angle_d0.9254121
X-RAY DIFFRACTIONf_dihedral_angle_d13.5691811
X-RAY DIFFRACTIONf_chiral_restr0.048451
X-RAY DIFFRACTIONf_plane_restr0.005512
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1004-2.18450.23211360.19682467X-RAY DIFFRACTION98
2.1845-2.28390.27681290.20592537X-RAY DIFFRACTION99
2.2839-2.40420.27981200.20772532X-RAY DIFFRACTION99
2.4042-2.55480.27311370.20952501X-RAY DIFFRACTION99
2.5548-2.75190.27241390.21542531X-RAY DIFFRACTION99
2.7519-3.02860.25121410.22052530X-RAY DIFFRACTION100
3.0286-3.46630.26491440.20962574X-RAY DIFFRACTION100
3.4663-4.3650.21791480.18532607X-RAY DIFFRACTION100
4.365-29.99870.2321360.19532636X-RAY DIFFRACTION96

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