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- PDB-1yz9: Crystal structure of RNase III mutant E110Q from Aquifex aeolicus... -

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Basic information

Entry
Database: PDB / ID: 1yz9
TitleCrystal structure of RNase III mutant E110Q from Aquifex aeolicus complexed with double stranded RNA at 2.1-Angstrom Resolution
Components
  • 5'-R(*CP*GP*AP*AP*CP*UP*UP*CP*GP*CP*G)-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: 2.1 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 28, 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 1.3Nov 10, 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 30, 2023Group: Data collection / Database references / Structure summary
Category: audit_author / chem_comp_atom ...audit_author / chem_comp_atom / chem_comp_bond / citation_author
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID
Revision 1.5Oct 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
C: 5'-R(*CP*GP*AP*AP*CP*UP*UP*CP*GP*CP*G)-3'
D: 5'-R(*CP*GP*AP*AP*CP*UP*UP*CP*GP*CP*G)-3'
E: 5'-R(*CP*GP*AP*AP*CP*UP*UP*CP*GP*CP*G)-3'
F: 5'-R(*CP*GP*AP*AP*CP*UP*UP*CP*GP*CP*G)-3'
A: Ribonuclease III
B: Ribonuclease III
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,89413
Polymers66,2216
Non-polymers6727
Water6,972387
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.586, 118.362, 61.900
Angle α, β, γ (deg.)90.00, 99.45, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: RNA chain
5'-R(*CP*GP*AP*AP*CP*UP*UP*CP*GP*CP*G)-3'


Mass: 3482.130 Da / Num. of mol.: 4 / Source method: obtained synthetically
#2: Protein Ribonuclease III / / RNase III


Mass: 26146.396 Da / Num. of mol.: 2 / Mutation: E110Q
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: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 387 / 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: 3.24 Å3/Da / Density % sol: 60.5 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Ammonium sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Components of the solutions
IDNameCrystal-IDSol-ID
1Ammonium sulfate11
2H2O11
3Ammonium sulfate12
4H2O12

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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: Aug 9, 2004 / Details: mirror
RadiationMonochromator: Silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→29.88 Å / Num. all: 42826 / Num. obs: 42826 / % possible obs: 85.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Biso Wilson estimate: 47.5 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 14.5
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.365 / Mean I/σ(I) obs: 2.56 / Num. unique all: 2512 / % possible all: 50.1

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Processing

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

1i4s


Resolution: 2.1→29.88 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 798953.27 / 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
Rfree0.238 2145 5 %RANDOM
Rwork0.208 ---
all0.21 42826 --
obs0.21 42826 85.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 56.1708 Å2 / ksol: 0.363276 e/Å3
Displacement parametersBiso mean: 52.7 Å2
Baniso -1Baniso -2Baniso -3
1--3.39 Å20 Å23.59 Å2
2--5.6 Å20 Å2
3----2.2 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.27 Å
Luzzati d res low-30 Å
Luzzati sigma a0.25 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 2.1→29.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3657 920 35 387 4999
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
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_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d17.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.93
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it3.461.5
X-RAY DIFFRACTIONc_mcangle_it4.712
X-RAY DIFFRACTIONc_scbond_it5.152
X-RAY DIFFRACTIONc_scangle_it7.082.5
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.334 213 5.1 %
Rwork0.29 3968 -
obs--50 %
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

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