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- PDB-1yyw: Crystal structure of RNase III from Aquifex aeolicus complexed wi... -

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Basic information

Entry
Database: PDB / ID: 1yyw
TitleCrystal structure of RNase III from Aquifex aeolicus complexed with double stranded RNA at 2.8-Angstrom Resolution
Components
  • 5'-R(*AP*AP*AP*UP*AP*UP*AP*UP*AP*UP*UP*U)-3'
  • Ribonuclease III
KeywordsHYDROLASE/RNA / Ribonuclease III / double-stranded RNA / RNA interference / endonucleolytic cleavage / 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 / identical protein binding / metal ion binding / cytoplasm
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 domain / Ribonuclease III family domain profile. / Ribonuclease III family / Ribonuclease III domain / Double Stranded RNA Binding Domain - #20 ...Ribonuclease III domain / Ribonuclease iii, N-terminal Endonuclease Domain; Chain A / Ribonuclease-III-like / Ribonuclease III / Ribonuclease III family signature. / Ribonuclease III domain / 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 speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsGan, J. / Tropea, J.E. / Austin, B.P. / Court, D.L. / Waugh, D.S. / Ji, X.
CitationJournal: Structure / Year: 2005
Title: Intermediate states of ribonuclease III in complex with double-stranded RNA
Authors: Gan, J. / Tropea, J.E. / Austin, B.P. / Court, D.L. / Waugh, D.S. / Ji, X.
History
DepositionFeb 25, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 22, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references / Structure summary
Category: audit_author / chem_comp_atom ...audit_author / chem_comp_atom / chem_comp_bond / citation_author / database_2
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 25, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
E: 5'-R(*AP*AP*AP*UP*AP*UP*AP*UP*AP*UP*UP*U)-3'
F: 5'-R(*AP*AP*AP*UP*AP*UP*AP*UP*AP*UP*UP*U)-3'
G: 5'-R(*AP*AP*AP*UP*AP*UP*AP*UP*AP*UP*UP*U)-3'
H: 5'-R(*AP*AP*AP*UP*AP*UP*AP*UP*AP*UP*UP*U)-3'
I: 5'-R(*AP*AP*AP*UP*AP*UP*AP*UP*AP*UP*UP*U)-3'
J: 5'-R(*AP*AP*AP*UP*AP*UP*AP*UP*AP*UP*UP*U)-3'
K: 5'-R(*AP*AP*AP*UP*AP*UP*AP*UP*AP*UP*UP*U)-3'
L: 5'-R(*AP*AP*AP*UP*AP*UP*AP*UP*AP*UP*UP*U)-3'
A: Ribonuclease III
B: Ribonuclease III
C: Ribonuclease III
D: Ribonuclease III


Theoretical massNumber of molelcules
Total (without water)134,72812
Polymers134,72812
Non-polymers00
Water1,69394
1
E: 5'-R(*AP*AP*AP*UP*AP*UP*AP*UP*AP*UP*UP*U)-3'
F: 5'-R(*AP*AP*AP*UP*AP*UP*AP*UP*AP*UP*UP*U)-3'
G: 5'-R(*AP*AP*AP*UP*AP*UP*AP*UP*AP*UP*UP*U)-3'
H: 5'-R(*AP*AP*AP*UP*AP*UP*AP*UP*AP*UP*UP*U)-3'
A: Ribonuclease III
B: Ribonuclease III


Theoretical massNumber of molelcules
Total (without water)67,3646
Polymers67,3646
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
I: 5'-R(*AP*AP*AP*UP*AP*UP*AP*UP*AP*UP*UP*U)-3'
J: 5'-R(*AP*AP*AP*UP*AP*UP*AP*UP*AP*UP*UP*U)-3'
K: 5'-R(*AP*AP*AP*UP*AP*UP*AP*UP*AP*UP*UP*U)-3'
L: 5'-R(*AP*AP*AP*UP*AP*UP*AP*UP*AP*UP*UP*U)-3'
C: Ribonuclease III
D: Ribonuclease III


Theoretical massNumber of molelcules
Total (without water)67,3646
Polymers67,3646
Non-polymers00
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.428, 95.906, 166.004
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: RNA chain
5'-R(*AP*AP*AP*UP*AP*UP*AP*UP*AP*UP*UP*U)-3'


Mass: 3767.272 Da / Num. of mol.: 8 / Source method: obtained synthetically
#2: Protein
Ribonuclease III / RNase III


Mass: 26147.381 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Gene: rnc / Plasmid: pHPK1409 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-RIL / References: UniProt: O67082, ribonuclease III
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / 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: 2.57 Å3/Da / Density % sol: 50.2 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: PEG4000, iso-propanol, tri-sodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG400011
2iso-propanol11
3tri-sodium citrate11
4H2O11
5PEG400012
6iso-propanol12
7tri-sodium citrate12
8H2O12

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: BRUKER PROTEUM 300 / Detector: CCD / Date: Dec 14, 2003 / Details: mirror
RadiationMonochromator: Silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→29.98 Å / Num. all: 31417 / Num. obs: 31417 / % possible obs: 90.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Biso Wilson estimate: 49.9 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 12.6
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.361 / Mean I/σ(I) obs: 1.2 / Num. unique all: 1526 / % possible all: 44.8

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB 1I4S

1i4s


Resolution: 2.8→29.98 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 141699.88 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.314 1878 6 %RANDOM
Rwork0.243 ---
all0.246 31417 --
obs0.246 31417 90.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 14.5893 Å2 / ksol: 0.277748 e/Å3
Displacement parametersBiso mean: 62.5 Å2
Baniso -1Baniso -2Baniso -3
1--0.71 Å20 Å20 Å2
2--4 Å20 Å2
3----3.29 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.56 Å0.42 Å
Luzzati d res low-30 Å
Luzzati sigma a0.54 Å0.5 Å
Refinement stepCycle: LAST / Resolution: 2.8→29.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7310 1992 0 94 9396
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1
X-RAY DIFFRACTIONc_dihedral_angle_d18.3
X-RAY DIFFRACTIONc_improper_angle_d1.07
X-RAY DIFFRACTIONc_mcbond_it3.731.5
X-RAY DIFFRACTIONc_mcangle_it6.132
X-RAY DIFFRACTIONc_scbond_it5.12
X-RAY DIFFRACTIONc_scangle_it7.432.5
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.405 205 6.5 %
Rwork0.388 2935 -
obs--55.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION5TRIS.PARAMTRIS.TOP

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