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- PDB-2qkb: Human RNase H catalytic domain mutant D210N in complex with 20-me... -

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Basic information

Entry
Database: PDB / ID: 2qkb
TitleHuman RNase H catalytic domain mutant D210N in complex with 20-mer RNA/DNA hybrid
Components
  • 5'-D(*DGP*DGP*DAP*DAP*DTP*DCP*DAP*DGP*DGP*DTP*DGP*DTP*DCP*DGP*DCP*DAP*DCP*DTP*DCP*DT)-3'
  • 5'-R(*GP*GP*AP*GP*UP*GP*CP*GP*AP*CP*AP*CP*CP*UP*GP*AP*UP*UP*CP*C)-3')
  • Ribonuclease H1
KeywordsHYDROLASE/DNA/RNA / RNase H / RNA/DNA hybrid / HYDROLASE-DNA-RNA COMPLEX
Function / homology
Function and homology information


Strand-asynchronous mitochondrial DNA replication / DNA replication, removal of RNA primer / RNA catabolic process / ribonuclease H / RNA nuclease activity / RNA-DNA hybrid ribonuclease activity / nucleic acid binding / magnesium ion binding / mitochondrion / RNA binding
Similarity search - Function
Ribonuclease H1, eukaryote / Ribonuclease H1, N-terminal / Ribonuclease H1, N-terminal domain superfamily / Ribonuclease H1 N-terminal domain / : / Ribonuclease H-like superfamily/Ribonuclease H / Ribosomal protein L9/RNase H1, N-terminal / RNase H / RNase H type-1 domain profile. / Ribonuclease H domain ...Ribonuclease H1, eukaryote / Ribonuclease H1, N-terminal / Ribonuclease H1, N-terminal domain superfamily / Ribonuclease H1 N-terminal domain / : / Ribonuclease H-like superfamily/Ribonuclease H / Ribosomal protein L9/RNase H1, N-terminal / RNase H / RNase H type-1 domain profile. / Ribonuclease H domain / 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 H1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsNowotny, M. / Gaidamakov, S.A. / Ghirlando, R. / Cerritelli, S.M. / Crouch, R.J. / Yang, W.
CitationJournal: Mol.Cell / Year: 2007
Title: Structure of Human RNase H1 Complexed with an RNA/DNA Hybrid: Insight into HIV Reverse Transcription
Authors: Nowotny, M. / Gaidamakov, S.A. / Ghirlando, R. / Cerritelli, S.M. / Crouch, R.J. / Yang, W.
History
DepositionJul 10, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 28, 2021Group: Database references / Derived calculations / Refinement description
Category: refine / struct_conn ...refine / struct_conn / struct_ref_seq_dif / struct_site
Item: _refine.ls_percent_reflns_obs / _refine.pdbx_ls_cross_valid_method ..._refine.ls_percent_reflns_obs / _refine.pdbx_ls_cross_valid_method / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.6Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: 5'-R(*GP*GP*AP*GP*UP*GP*CP*GP*AP*CP*AP*CP*CP*UP*GP*AP*UP*UP*CP*C)-3')
D: 5'-D(*DGP*DGP*DAP*DAP*DTP*DCP*DAP*DGP*DGP*DTP*DGP*DTP*DCP*DGP*DCP*DAP*DCP*DTP*DCP*DT)-3'
A: Ribonuclease H1
B: Ribonuclease H1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,4338
Polymers47,1174
Non-polymers3164
Water1,04558
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)109.991, 109.991, 67.253
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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RNA chain / DNA chain / Protein , 3 types, 4 molecules CDAB

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


Mass: 6382.854 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 5'-D(*DGP*DGP*DAP*DAP*DTP*DCP*DAP*DGP*DGP*DTP*DGP*DTP*DCP*DGP*DCP*DAP*DCP*DTP*DCP*DT)-3'


Mass: 6149.978 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein Ribonuclease H1 / E.C.3.1.26.4 / Hs-RNase HC / RNase H1 / Ribonuclease H type II


Mass: 17291.861 Da / Num. of mol.: 2 / Fragment: C-terminal domain (residues 134-286) / Mutation: D210N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RNASEH1, RNH1 / Plasmid: pET15 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: O60930, ribonuclease H

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Non-polymers , 3 types, 62 molecules

#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.49 Å3/Da / Density % sol: 50.63 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 15% PEG 3350, 0.1 M LiSO4, 0.1 M Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 335011
2LiSO411
3Tris11
4PEG 335012
5LiSO412
6Tris12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→40 Å / Num. all: 18670 / Num. obs: 16949 / % possible obs: 90.8 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 35.8
Reflection shellResolution: 2.4→2.49 Å / Rmerge(I) obs: 0.452 / Mean I/σ(I) obs: 2.7

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QK9

2qk9


Resolution: 2.4→40 Å / Cross valid method: FREE R-VALUE / Stereochemistry target values: Engh & Huber
Details: The last round of refinement in CNS was carried out with the pucker restraints for the DNA strand removed
RfactorNum. reflection% reflectionSelection details
Rfree0.255 1680 -Random
Rwork0.2076 ---
all-18670 --
obs-16949 90.8 %-
Displacement parametersBiso mean: 59.3 Å2
Refinement stepCycle: LAST / Resolution: 2.4→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2356 812 18 58 3244
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.012894
X-RAY DIFFRACTIONc_angle_deg1.74222
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_mcbond_it1.8791.5
X-RAY DIFFRACTIONc_mcangle_it3.2762
X-RAY DIFFRACTIONc_scbond_it2.2622
X-RAY DIFFRACTIONc_scangle_it3.3752.5

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