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- PDB-5f3o: Crystal structure of EhRNaseIII229 from Entamoeba histolytica com... -

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Basic information

Entry
Database: PDB / ID: 5f3o
TitleCrystal structure of EhRNaseIII229 from Entamoeba histolytica complexed with Mn2+
ComponentsPutative uncharacterized protein
KeywordsRNA BINDING PROTEIN / RNaseIII / non canonical 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 / Resolution: 2.05 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 28, 2016Provider: 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)46,0906
Polymers45,7882
Non-polymers3024
Water1,802100
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3000 Å2
ΔGint-47 kcal/mol
Surface area17940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.329, 89.729, 100.196
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: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.29 Å3/Da / Density % sol: 46.18 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 1.6M (NH4)2SO4, 0.01M MgCl2, 0.05M Tris-HCl pH 7.5

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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: Apr 24, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 25785 / % possible obs: 95.3 % / Redundancy: 5.5 % / Net I/σ(I): 16.4

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Processing

Software
NameVersionClassification
HKL-2000data processing
Cootmodel building
PHENIX(1.10_2155)refinement
RefinementResolution: 2.05→44.864 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 23.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2401 1292 5.04 %
Rwork0.1971 --
obs0.1992 25617 94.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.05→44.864 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3175 0 12 100 3287
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033262
X-RAY DIFFRACTIONf_angle_d0.5744407
X-RAY DIFFRACTIONf_dihedral_angle_d14.3621944
X-RAY DIFFRACTIONf_chiral_restr0.032478
X-RAY DIFFRACTIONf_plane_restr0.003555
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0471-2.12910.30931340.24892769X-RAY DIFFRACTION98
2.1291-2.2260.28241540.21252786X-RAY DIFFRACTION100
2.226-2.34340.27591090.21121811X-RAY DIFFRACTION65
2.3434-2.49020.24621380.18962819X-RAY DIFFRACTION100
2.4902-2.68240.23341570.19182837X-RAY DIFFRACTION100
2.6824-2.95230.24531490.19972834X-RAY DIFFRACTION100
2.9523-3.37940.26381570.21162844X-RAY DIFFRACTION100
3.3794-4.25710.24091560.19262584X-RAY DIFFRACTION90
4.2571-44.87530.19191380.18063041X-RAY DIFFRACTION99

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