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- PDB-7r97: Crystal structure of postcleavge complex of Escherichia coli RNase III -

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Basic information

Entry
Database: PDB / ID: 7r97
TitleCrystal structure of postcleavge complex of Escherichia coli RNase III
Components
  • RNA (28-MER)
  • Ribonuclease 3
KeywordsHYDROLASE/RNA / protein-RNA complex / HYDROLASE-RNA complex
Function / homology
Function and homology information


ribonuclease III / ribonuclease III activity / tRNA processing / RNA processing / mRNA processing / rRNA processing / double-stranded RNA binding / regulation of gene expression / rRNA binding / enzyme binding ...ribonuclease III / ribonuclease III activity / tRNA processing / RNA processing / mRNA processing / rRNA processing / double-stranded RNA binding / regulation of gene expression / rRNA binding / enzyme binding / magnesium ion binding / protein homodimerization activity / ATP binding / cytosol
Similarity search - Function
Ribonuclease III domain / Ribonuclease iii, N-terminal Endonuclease Domain; Chain A / Ribonuclease-III-like / Ribonuclease III / Ribonuclease III family signature. / Ribonuclease III family domain profile. / Ribonuclease III family / Ribonuclease III domain / Double Stranded RNA Binding Domain - #20 / Double-stranded RNA binding motif ...Ribonuclease III domain / Ribonuclease iii, N-terminal Endonuclease Domain; Chain A / Ribonuclease-III-like / Ribonuclease III / Ribonuclease III family signature. / Ribonuclease III family domain profile. / Ribonuclease III family / Ribonuclease III domain / Double Stranded RNA Binding Domain - #20 / Double-stranded RNA binding motif / Double-stranded RNA binding motif / Ribonuclease III, endonuclease domain superfamily / Double stranded RNA-binding domain (dsRBD) profile. / Double-stranded RNA-binding domain / Double Stranded RNA Binding Domain / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / RNA / RNA (> 10) / Ribonuclease 3
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.804 Å
AuthorsDharavath, S. / Shaw, G.X. / Ji, X.
Citation
Journal: Rna Biol. / Year: 2022
Title: Structural basis for Dicer-like function of an engineered RNase III variant and insights into the reaction trajectory of two-Mg 2+ -ion catalysis.
Authors: Dharavath, S. / Shaw, G.X. / Ji, X.
#1: Journal: Nucleic Acids Res. / Year: 2019
Title: The molecular mechanism of dsRNA processing by a bacterial Dicer
Authors: Jin, L. / Song, H. / Tropea, J.E. / Danielle, N. / Waugh, D. / Gu, S. / Ji, X.
History
DepositionJun 28, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ribonuclease 3
B: Ribonuclease 3
C: RNA (28-MER)
D: RNA (28-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,37235
Polymers68,7874
Non-polymers1,58531
Water7,530418
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14490 Å2
ΔGint-194 kcal/mol
Surface area26490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.929, 65.753, 84.519
Angle α, β, γ (deg.)90.000, 102.090, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein / RNA chain , 2 types, 4 molecules ABCD

#1: Protein Ribonuclease 3 / Ribonuclease III / RNase III


Mass: 25412.938 Da / Num. of mol.: 2 / Fragment: Full-length / Mutation: E38A, E65A, Q165A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: rnc, b2567, JW2551 / Plasmid: pDEST-HisMBP-EcRNaseIIIEEQ / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): CodonPlus-RIL / References: UniProt: P0A7Y0, ribonuclease III
#2: RNA chain RNA (28-MER)


Mass: 8980.364 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)

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Non-polymers , 6 types, 449 molecules

#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#7: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 418 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.25 Å3/Da / Density % sol: 45.3 % / Mosaicity: 0.699 °
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.4 / Details: PEG 3350, KBr, etc.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Mar 15, 2019 / Details: mirrors
RadiationMonochromator: Double crystal / Protocol: 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: 55901 / % possible obs: 99.5 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.121 / Rpim(I) all: 0.053 / Rrim(I) all: 0.132 / Χ2: 0.986 / Net I/σ(I): 10.7 / Num. measured all: 362726
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.8-1.866.11.15154940.6080.5041.2610.9998.4
1.86-1.946.90.88155870.840.3620.9541.02399.9
1.94-2.036.90.5855920.9190.2380.6271.04999.8
2.03-2.136.80.36955550.9630.1530.41.02499.9
2.13-2.276.60.25956050.9750.1090.2811.03499.9
2.27-2.446.30.17755770.9850.0770.1931.02999.8
2.44-2.695.90.12455740.9860.0560.1361.04299.1
2.69-3.0870.09255880.9950.0380.10.99999.9
3.08-3.886.50.06856320.9960.030.0740.87599.6
3.88-305.90.06556970.9930.030.0720.77499.1

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.16refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2NUG

2nug


Resolution: 1.804→28.308 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2021 1000 1.79 %
Rwork0.171 54856 -
obs0.1716 55856 99.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 85.14 Å2 / Biso mean: 27.6969 Å2 / Biso min: 9.7 Å2
Refinement stepCycle: final / Resolution: 1.804→28.308 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3572 1196 171 418 5357
Biso mean--41.68 32.55 -
Num. residues----508
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085074
X-RAY DIFFRACTIONf_angle_d1.0187104
X-RAY DIFFRACTIONf_dihedral_angle_d11.1772960
X-RAY DIFFRACTIONf_chiral_restr0.054836
X-RAY DIFFRACTIONf_plane_restr0.006715
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.804-1.89890.26541380.2148757396
1.8989-2.01780.23981430.1937859100
2.0178-2.17360.20951430.17567859100
2.1736-2.39220.18441440.16887862100
2.3922-2.73810.20091420.1665784499
2.7381-3.44880.19921450.17187884100
3.4488-28.3080.19241450.1619797599

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