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- PDB-1rc7: Crystal structure of RNase III Mutant E110K from Aquifex Aeolicus... -

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Basic information

Entry
Database: PDB / ID: 1rc7
TitleCrystal structure of RNase III Mutant E110K from Aquifex Aeolicus complexed with ds-RNA at 2.15 Angstrom Resolution
Components
  • 5'-R(*GP*GP*CP*GP*CP*GP*CP*GP*CP*C)-3'
  • Ribonuclease III
KeywordsHYDROLASE/RNA / Ribonuclease III / ds-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 / Ribonuclease 3
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsBlaszczyk, J. / Gan, J. / Ji, X.
Citation
Journal: Structure / Year: 2004
Title: Noncatalytic Assembly of Ribonuclease III with Double-Stranded RNA.
Authors: Blaszczyk, J. / Gan, J. / Tropea, J.E. / Court, D.L. / Waugh, D.S. / Ji, X.
#1: Journal: Structure / Year: 2001
Title: Crystallographic and Modelling Studies of RNase III Suggest a Mechanism for Double-Stranded RNA Cleavage
Authors: Blaszczyk, J. / Tropea, J.E. / Bubunenko, M. / Routzahn, K.M. / Waugh, D.S. / Court, D.L. / Ji, X.
History
DepositionNov 3, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Aug 30, 2023Group: Database references / Structure summary / Category: audit_author / citation_author
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: 5'-R(*GP*GP*CP*GP*CP*GP*CP*GP*CP*C)-3'
C: 5'-R(*GP*GP*CP*GP*CP*GP*CP*GP*CP*C)-3'
D: 5'-R(*GP*GP*CP*GP*CP*GP*CP*GP*CP*C)-3'
E: 5'-R(*GP*GP*CP*GP*CP*GP*CP*GP*CP*C)-3'
A: Ribonuclease III
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9686
Polymers38,8465
Non-polymers1221
Water4,252236
1
B: 5'-R(*GP*GP*CP*GP*CP*GP*CP*GP*CP*C)-3'
C: 5'-R(*GP*GP*CP*GP*CP*GP*CP*GP*CP*C)-3'
D: 5'-R(*GP*GP*CP*GP*CP*GP*CP*GP*CP*C)-3'
E: 5'-R(*GP*GP*CP*GP*CP*GP*CP*GP*CP*C)-3'
A: Ribonuclease III
hetero molecules

B: 5'-R(*GP*GP*CP*GP*CP*GP*CP*GP*CP*C)-3'
C: 5'-R(*GP*GP*CP*GP*CP*GP*CP*GP*CP*C)-3'
D: 5'-R(*GP*GP*CP*GP*CP*GP*CP*GP*CP*C)-3'
E: 5'-R(*GP*GP*CP*GP*CP*GP*CP*GP*CP*C)-3'
A: Ribonuclease III
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,93712
Polymers77,69310
Non-polymers2442
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_575x,-y+2,-z1
Unit cell
Length a, b, c (Å)58.286, 118.142, 106.665
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-319-

HOH

21A-329-

HOH

31A-435-

HOH

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Components

#1: RNA chain
5'-R(*GP*GP*CP*GP*CP*GP*CP*GP*CP*C)-3'


Mass: 3206.981 Da / Num. of mol.: 4 / Source method: obtained synthetically
#2: Protein Ribonuclease III / / 3.1.26.3 / RNase III


Mass: 26018.334 Da / Num. of mol.: 1 / Mutation: E110K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Gene: RNC, AQ_946 / Plasmid: pDONR201, pDEST-42 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O67082, ribonuclease III
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 236 / Fragment: Tris(hydroxymethyl)-aminomethane / 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: 2.356 Å3/Da / Density % sol: 45.79 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG4000, Tris-HCl, Sodium Chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG400011
2Tris-HClTris11
3NaClSodium chloride11
4NaClSodium chloride12
5PEG400012

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: BRUKER PROTEUM 300 / Detector: CCD / Date: Jul 5, 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: 2.15→28.47 Å / Num. all: 20431 / Num. obs: 18715 / % possible obs: 91.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.05 % / Biso Wilson estimate: 44.7 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 22
Reflection shellResolution: 2.15→2.28 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.262 / Mean I/σ(I) obs: 1.8 / % possible all: 71.2

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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: 2.15→28.47 Å / Rfactor Rfree error: 0.007 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.242 1091 5.8 %RANDOM
Rwork0.192 ---
obs0.192 18715 91.6 %-
all-20431 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 54.9941 Å2 / ksol: 0.345107 e/Å3
Displacement parametersBiso mean: 47.2 Å2
Baniso -1Baniso -2Baniso -3
1-5.42 Å20 Å20 Å2
2---4.31 Å20 Å2
3----1.11 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.26 Å
Luzzati d res low-30 Å
Luzzati sigma a0.37 Å0.29 Å
Refinement stepCycle: LAST / Resolution: 2.15→28.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1838 848 8 236 2930
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
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_deg1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d15.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.96
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it3.471.5
X-RAY DIFFRACTIONc_mcangle_it4.292
X-RAY DIFFRACTIONc_scbond_it4.992
X-RAY DIFFRACTIONc_scangle_it6.452.5
LS refinement shellResolution: 2.15→2.28 Å / Rfactor Rfree error: 0.036 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.421 135 5.7 %
Rwork0.323 2251 -
obs--71.2 %
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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