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- PDB-2qk9: Human RNase H catalytic domain mutant D210N in complex with 18-me... -

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Basic information

Entry
Database: PDB / ID: 2qk9
TitleHuman RNase H catalytic domain mutant D210N in complex with 18-mer RNA/DNA hybrid
Components
  • 5'-D(*GP*GP*AP*AP*TP*CP*AP*GP*GP*TP*GP*TP*CP*GP*CP*AP*CP*T)-3'
  • 5'-R(*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
HEXANE-1,6-DIAMINE / CITRATE ANION / DNA / DNA (> 10) / RNA / RNA (> 10) / Ribonuclease H1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 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: Non-polymer description / Version format compliance
Revision 1.2Oct 20, 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 1.3Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: 5'-R(*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*T)-3'
A: Ribonuclease H1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,55415
Polymers28,3693
Non-polymers1,18512
Water1,964109
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)158.578, 158.578, 142.055
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

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

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


Mass: 5708.443 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 5'-D(*GP*GP*AP*AP*TP*CP*AP*GP*GP*TP*GP*TP*CP*GP*CP*AP*CP*T)-3'


Mass: 5556.603 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: 17104.279 Da / Num. of mol.: 1 / 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 , 6 types, 121 molecules

#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-16D / HEXANE-1,6-DIAMINE / 1,6-DIAMINOHEXANE


Mass: 116.205 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H16N2
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#8: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / 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

Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 1.5 M ammonium sulfate, 0.1 M Na citrate (pH 5.6) 20mM ATP or 3% 1,6-diaminohexane, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Components of the solutions
IDNameCrystal-IDSol-ID
1(NH4)2SO411
2sodium citrate11
31,6-diaminohexane11
4(NH4)2SO412
5sodium citrate12
61,6-diaminohexane12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.55→30 Å / Num. all: 22505 / Num. obs: 21164 / % possible obs: 94 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 38.7
Reflection shellResolution: 2.55→2.64 Å / Rmerge(I) obs: 0.456 / Mean I/σ(I) obs: 4.1

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Original low resolution strcture solved with the same crystal and SeMet SIRAS

Resolution: 2.55→30 Å / 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
Rfree0.216 2085 -Random
Rwork0.19 ---
all-22505 --
obs-21164 94 %-
Displacement parametersBiso mean: 43.3 Å2
Refinement stepCycle: LAST / Resolution: 2.55→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1188 746 69 109 2112
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.013483
X-RAY DIFFRACTIONc_angle_deg1.86942
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_mcbond_it1.4181.5
X-RAY DIFFRACTIONc_mcangle_it2.4372
X-RAY DIFFRACTIONc_scbond_it1.9042
X-RAY DIFFRACTIONc_scangle_it2.9082.5

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