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- PDB-4h8k: Crystal structure of LC11-RNase H1 in complex with RNA/DNA hybrid -

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Basic information

Entry
Database: PDB / ID: 4h8k
TitleCrystal structure of LC11-RNase H1 in complex with RNA/DNA hybrid
Components
  • DNA (5'-D(*GP*GP*AP*AP*TP*CP*AP*GP*GP*TP*GP*TP*CP*G)-3')
  • RNA (5'-R(*CP*GP*AP*CP*AP*CP*CP*UP*GP*AP*UP*UP*CP*C)-3')
  • Ribonuclease H
KeywordsHydrolase/DNA/RNA / RNase H / Ribonuclease H RNA DNA Hybrid / Hydrolase / Ribonuclease H / Hydrolase-DNA-RNA complex
Function / homology
Function and homology information


ribonuclease H / RNA-DNA hybrid ribonuclease activity / nucleic acid binding
Similarity search - Function
Reverse transcriptase-like / Ribonuclease H-like superfamily/Ribonuclease H / Ribonuclease H domain / RNase H type-1 domain profile. / 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 H
Similarity search - Component
Biological speciesuncultured organism (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsNguyen, T.N. / You, D.J. / Matsumoto, H. / Kanaya, E. / Kanaya, S.
CitationJournal: J.Struct.Biol. / Year: 2013
Title: Crystal structure of metagenome-derived LC11-RNase H1 in complex with RNA/DNA hybrid
Authors: Nguyen, T.N. / You, D.J. / Matsumoto, H. / Kanaya, E. / Koga, Y. / Kanaya, S.
History
DepositionSep 23, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 25, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ribonuclease H
B: Ribonuclease H
C: RNA (5'-R(*CP*GP*AP*CP*AP*CP*CP*UP*GP*AP*UP*UP*CP*C)-3')
D: DNA (5'-D(*GP*GP*AP*AP*TP*CP*AP*GP*GP*TP*GP*TP*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)40,0054
Polymers40,0054
Non-polymers00
Water1,65792
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5020 Å2
ΔGint-45 kcal/mol
Surface area16470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.613, 90.758, 55.605
Angle α, β, γ (deg.)90.00, 97.82, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Ribonuclease H / / LC11-RNase H1


Mass: 15630.956 Da / Num. of mol.: 2 / Mutation: D77N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) uncultured organism (environmental samples)
Plasmid: pET25b / Production host: Escherichia coli (E. coli) / Strain (production host): MIC2067(DE3) / References: UniProt: E0X767, ribonuclease H
#2: RNA chain RNA (5'-R(*CP*GP*AP*CP*AP*CP*CP*UP*GP*AP*UP*UP*CP*C)-3')


Mass: 4382.659 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This sequence occurs naturally in bacteria
#3: DNA chain DNA (5'-D(*GP*GP*AP*AP*TP*CP*AP*GP*GP*TP*GP*TP*CP*G)-3')


Mass: 4360.840 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This sequence occurs naturally in bacteria
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 92 / 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: 2.66 Å3/Da / Density % sol: 53.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2M ammonium acetate, 0.1M Tris, 25% PEG3350, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: BRUKER SMART 6500 / Detector: CCD / Date: Nov 13, 2011
RadiationMonochromator: horizontal focusing mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 17868 / % possible obs: 95.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.4 % / Rmerge(I) obs: 0.049 / Rsym value: 0.049 / Net I/σ(I): 42.556
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allDiffraction-ID% possible all
2.3-2.346.80.225.72782182.1
2.34-2.386.90.2115.78797186
2.38-2.436.90.2015.89813188
2.43-2.487.10.1726.01857192.5
2.48-2.537.20.1616.45870192.1
2.53-2.597.40.146.42897198

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3U3G

3u3g


Resolution: 2.3→38.28 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.908 / SU B: 7.64 / SU ML: 0.187 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.349 / ESU R Free: 0.27 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27785 919 5.2 %RANDOM
Rwork0.20658 ---
all0.21025 ---
obs0.21025 16914 95.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 52.048 Å2
Baniso -1Baniso -2Baniso -3
1--3.2 Å2-0 Å21.35 Å2
2---3.68 Å2-0 Å2
3---7.25 Å2
Refinement stepCycle: LAST / Resolution: 2.3→38.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2156 579 0 92 2827
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.007
X-RAY DIFFRACTIONr_angle_refined_deg1.053
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.555
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.912
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.947
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.239
X-RAY DIFFRACTIONr_chiral_restr0.075
X-RAY DIFFRACTIONr_gen_planes_refined0.017
X-RAY DIFFRACTIONr_mcbond_it1.554
X-RAY DIFFRACTIONr_mcangle_it2.702
X-RAY DIFFRACTIONr_scbond_it
LS refinement shellResolution: 2.299→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 63 -
Rwork0.281 1079 -
obs--82.22 %

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