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- PDB-4py5: Thermovibrio ammonificans RNase H3 in complex with 19-mer RNA/DNA -

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Basic information

Entry
Database: PDB / ID: 4py5
TitleThermovibrio ammonificans RNase H3 in complex with 19-mer RNA/DNA
Components
  • 5'-D(*GP*GP*AP*AP*TP*CP*AP*GP*GP*TP*GP*TP*CP*GP*CP*AP*CP*TP*C)-3'
  • 5'-R(*GP*AP*GP*UP*GP*CP*GP*AP*CP*AP*CP*CP*UP*GP*AP*UP*UP*CP*C)-3'
  • Ribonuclease
KeywordsHydrolase/DNA/RNA / RNase H fold / RNA/DNA hybrid / Hydrolase-DNA-RNA complex
Function / homology
Function and homology information


ribonuclease H / RNA-DNA hybrid ribonuclease activity / RNA binding / metal ion binding / cytoplasm
Similarity search - Function
Ribonuclease HIII / Ribonuclease HII/HIII / Ribonuclease HII/HIII domain / Ribonuclease HII / TATA-Binding Protein / TATA-Binding Protein / TBP domain superfamily / Ribonuclease H-like superfamily/Ribonuclease H / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily ...Ribonuclease HIII / Ribonuclease HII/HIII / Ribonuclease HII/HIII domain / Ribonuclease HII / TATA-Binding Protein / TATA-Binding Protein / TBP domain superfamily / Ribonuclease H-like superfamily/Ribonuclease H / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / RNA / RNA (> 10) / Ribonuclease
Similarity search - Component
Biological speciesThermovibrio ammonificans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsFigiel, M. / Nowotny, M.
CitationJournal: Nucleic Acids Res. / Year: 2014
Title: Crystal structure of RNase H3-substrate complex reveals parallel evolution of RNA/DNA hybrid recognition.
Authors: Figiel, M. / Nowotny, M.
History
DepositionMar 26, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 30, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 27, 2014Group: Database references
Revision 1.2Oct 29, 2014Group: Structure summary

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)42,99012
Polymers42,2013
Non-polymers7899
Water3,369187
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6500 Å2
ΔGint-125 kcal/mol
Surface area16530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.449, 67.661, 107.514
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / RNA chain / DNA chain , 3 types, 3 molecules ABC

#1: Protein Ribonuclease


Mass: 30301.682 Da / Num. of mol.: 1 / Mutation: D78N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermovibrio ammonificans (bacteria) / Strain: HB-1 / Gene: Theam_0945 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Star
References: UniProt: E8T217, Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters
#2: RNA chain 5'-R(*GP*AP*GP*UP*GP*CP*GP*AP*CP*AP*CP*CP*UP*GP*AP*UP*UP*CP*C)-3'


Mass: 6053.649 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain 5'-D(*GP*GP*AP*AP*TP*CP*AP*GP*GP*TP*GP*TP*CP*GP*CP*AP*CP*TP*C)-3'


Mass: 5845.785 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Non-polymers , 4 types, 196 molecules

#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 187 / 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: 2.52 Å3/Da / Density % sol: 51.17 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2 M AmSO4, 0.1 M BisTris, 25% PEG 3350, 10 mM spermine tetrahydrochloride, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jan 31, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 25583 / Num. obs: 25396 / % possible obs: 99.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.069
Reflection shellResolution: 2.1→2.23 Å / Redundancy: 4.27 % / Rmerge(I) obs: 0.564 / Mean I/σ(I) obs: 2.66 / Num. unique all: 3890 / % possible all: 95.7

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Processing

Software
NameVersionClassification
PHENIXAutoSolmodel building
PHENIX(phenix.refine: 1.8.1_1168)refinement
XDSdata reduction
XDSdata scaling
PHENIXAutoSolphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→42.09 Å / SU ML: 0.24 / σ(F): 1.38 / Phase error: 23.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.233 1271 5.01 %random
Rwork0.1832 ---
obs0.1857 25392 99.27 %-
all-25583 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→42.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2025 788 42 187 3042
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072978
X-RAY DIFFRACTIONf_angle_d1.0744194
X-RAY DIFFRACTIONf_dihedral_angle_d13.2981197
X-RAY DIFFRACTIONf_chiral_restr0.058503
X-RAY DIFFRACTIONf_plane_restr0.004392
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1001-2.18420.31351340.23912518X-RAY DIFFRACTION94
2.1842-2.28360.25951370.20682610X-RAY DIFFRACTION100
2.2836-2.40390.23091410.19662672X-RAY DIFFRACTION100
2.4039-2.55450.26421400.19592669X-RAY DIFFRACTION100
2.5545-2.75170.29711400.20952666X-RAY DIFFRACTION100
2.7517-3.02860.261420.20712684X-RAY DIFFRACTION100
3.0286-3.46670.23861420.18822713X-RAY DIFFRACTION100
3.4667-4.36690.19511440.15742730X-RAY DIFFRACTION100
4.3669-42.09820.21221510.16882859X-RAY DIFFRACTION100

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