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- PDB-2nue: Crystal structure of RNase III from Aquifex aeolicus complexed wi... -

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Basic information

Entry
Database: PDB / ID: 2nue
TitleCrystal structure of RNase III from Aquifex aeolicus complexed with ds-RNA at 2.9-Angstrom Resolution
Components
  • 46-MER
  • Ribonuclease III
Keywordshydrolase/RNA / Ribonuclease III / dsRNA / 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: 2.9 Å
AuthorsGan, J.H. / Shaw, G. / Tropea, J.E. / Waugh, D.S. / Court, D.L. / Ji, X.
CitationJournal: Mol.Microbiol. / Year: 2007
Title: A stepwise model for double-stranded RNA processing by ribonuclease III.
Authors: Gan, J. / Shaw, G. / Tropea, J.E. / Waugh, D.S. / Court, D.L. / Ji, X.
History
DepositionNov 9, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: audit_author / chem_comp_atom ...audit_author / chem_comp_atom / chem_comp_bond / citation_author / database_2 / pdbx_initial_refinement_model
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: 46-MER
A: Ribonuclease III
B: Ribonuclease III


Theoretical massNumber of molelcules
Total (without water)67,1143
Polymers67,1143
Non-polymers00
Water50428
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)101.596, 101.657, 67.082
Angle α, β, γ (deg.)90.00, 103.69, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: RNA chain 46-MER


Mass: 14818.836 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Protein Ribonuclease III / / RNase III


Mass: 26147.381 Da / Num. of mol.: 2
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 / Water


Mass: 18.015 Da / Num. of mol.: 28 / 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: 2.51 Å3/Da / Density % sol: 50.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2 M NaCl + 16% PEG3350 in 0.1 M Tris-Cl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1NaClSodium chloride11
2PEG335011
3Tris-Cl11
4H2O11
5NaClSodium chloride12
6PEG335012
7H2O12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jan 18, 2005 / Details: mirror
RadiationMonochromator: Silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→30 Å / Num. all: 13199 / Num. obs: 13199 / % possible obs: 89.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Biso Wilson estimate: 72.4 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 13.3
Reflection shellResolution: 2.9→3 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.16 / Mean I/σ(I) obs: 3.4 / % possible all: 53.4

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Processing

Software
NameVersionClassification
CNS1refinement
MAR345data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RC7

1rc7


Resolution: 2.9→29.11 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 935262.42 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.275 669 5.1 %RANDOM
Rwork0.238 ---
obs0.238 13142 89.1 %-
all-13142 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 35.1746 Å2 / ksol: 0.302101 e/Å3
Displacement parametersBiso mean: 98.4 Å2
Baniso -1Baniso -2Baniso -3
1-21.63 Å20 Å25.75 Å2
2---0.29 Å20 Å2
3----21.35 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.53 Å0.42 Å
Luzzati d res low-30 Å
Luzzati sigma a0.36 Å0.34 Å
Refinement stepCycle: LAST / Resolution: 2.9→29.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3677 980 0 28 4685
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg0.8
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d16.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.86
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it3.041.5
X-RAY DIFFRACTIONc_mcangle_it4.852
X-RAY DIFFRACTIONc_scbond_it5.522
X-RAY DIFFRACTIONc_scangle_it8.182.5
LS refinement shellResolution: 2.9→3.08 Å / Rfactor Rfree error: 0.041 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.364 79 5.2 %
Rwork0.347 1427 -
obs--61.8 %
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.partris.top

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