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- PDB-2qkk: Human RNase H catalytic domain mutant D210N in complex with 14-me... -

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Basic information

Entry
Database: PDB / ID: 2qkk
TitleHuman RNase H catalytic domain mutant D210N in complex with 14-mer RNA/DNA hybrid
Components
  • 5'-D(*GP*GP*AP*AP*TP*CP*AP*GP*GP*TP*GP*TP*CP*G)-3'
  • 5'-R(*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 / mitochondrial matrix / 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: 3.2 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 11, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / 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*CP*AP*CP*CP*UP*GP*AP*UP*UP*CP*C)-3'
D: 5'-D(*GP*GP*AP*AP*TP*CP*AP*GP*GP*TP*GP*TP*CP*G)-3'
G: 5'-R(*CP*GP*AP*CP*AP*CP*CP*UP*GP*AP*UP*UP*CP*C)-3'
H: 5'-D(*GP*GP*AP*AP*TP*CP*AP*GP*GP*TP*GP*TP*CP*G)-3'
K: 5'-R(*CP*GP*AP*CP*AP*CP*CP*UP*GP*AP*UP*UP*CP*C)-3'
L: 5'-D(*GP*GP*AP*AP*TP*CP*AP*GP*GP*TP*GP*TP*CP*G)-3'
O: 5'-R(*CP*GP*AP*CP*AP*CP*CP*UP*GP*AP*UP*UP*CP*C)-3'
P: 5'-D(*GP*GP*AP*AP*TP*CP*AP*GP*GP*TP*GP*TP*CP*G)-3'
T: 5'-R(*CP*GP*AP*CP*AP*CP*CP*UP*GP*AP*UP*UP*CP*C)-3'
U: 5'-D(*GP*GP*AP*AP*TP*CP*AP*GP*GP*TP*GP*TP*CP*G)-3'
X: 5'-R(*CP*GP*AP*CP*AP*CP*CP*UP*GP*AP*UP*UP*CP*C)-3'
Z: 5'-D(*GP*GP*AP*AP*TP*CP*AP*GP*GP*TP*GP*TP*CP*G)-3'
A: Ribonuclease H1
B: Ribonuclease H1
E: Ribonuclease H1
F: Ribonuclease H1
I: Ribonuclease H1
J: Ribonuclease H1
M: Ribonuclease H1
N: Ribonuclease H1
R: Ribonuclease H1
S: Ribonuclease H1
W: Ribonuclease H1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)241,52240
Polymers240,60823
Non-polymers91417
Water3,099172
1
C: 5'-R(*CP*GP*AP*CP*AP*CP*CP*UP*GP*AP*UP*UP*CP*C)-3'
D: 5'-D(*GP*GP*AP*AP*TP*CP*AP*GP*GP*TP*GP*TP*CP*G)-3'
A: Ribonuclease H1
B: Ribonuclease H1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,42510
Polymers42,9524
Non-polymers4736
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
G: 5'-R(*CP*GP*AP*CP*AP*CP*CP*UP*GP*AP*UP*UP*CP*C)-3'
H: 5'-D(*GP*GP*AP*AP*TP*CP*AP*GP*GP*TP*GP*TP*CP*G)-3'
E: Ribonuclease H1
F: Ribonuclease H1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,0727
Polymers42,9524
Non-polymers1203
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
K: 5'-R(*CP*GP*AP*CP*AP*CP*CP*UP*GP*AP*UP*UP*CP*C)-3'
L: 5'-D(*GP*GP*AP*AP*TP*CP*AP*GP*GP*TP*GP*TP*CP*G)-3'
I: Ribonuclease H1
J: Ribonuclease H1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,0326
Polymers42,9524
Non-polymers802
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
O: 5'-R(*CP*GP*AP*CP*AP*CP*CP*UP*GP*AP*UP*UP*CP*C)-3'
P: 5'-D(*GP*GP*AP*AP*TP*CP*AP*GP*GP*TP*GP*TP*CP*G)-3'
M: Ribonuclease H1
N: Ribonuclease H1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,0727
Polymers42,9524
Non-polymers1203
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
T: 5'-R(*CP*GP*AP*CP*AP*CP*CP*UP*GP*AP*UP*UP*CP*C)-3'
U: 5'-D(*GP*GP*AP*AP*TP*CP*AP*GP*GP*TP*GP*TP*CP*G)-3'
R: Ribonuclease H1
S: Ribonuclease H1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,0326
Polymers42,9524
Non-polymers802
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
X: 5'-R(*CP*GP*AP*CP*AP*CP*CP*UP*GP*AP*UP*UP*CP*C)-3'
Z: 5'-D(*GP*GP*AP*AP*TP*CP*AP*GP*GP*TP*GP*TP*CP*G)-3'
W: Ribonuclease H1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8884
Polymers25,8483
Non-polymers401
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)151.065, 176.200, 125.845
Angle α, β, γ (deg.)90.00, 90.22, 90.00
Int Tables number5
Space group name H-MC121

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Components

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RNA chain / DNA chain / Protein , 3 types, 23 molecules CGKOTXDHLPUZABEFIJMNRSW

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


Mass: 4382.659 Da / Num. of mol.: 6 / Source method: obtained synthetically
#2: DNA chain
5'-D(*GP*GP*AP*AP*TP*CP*AP*GP*GP*TP*GP*TP*CP*G)-3'


Mass: 4360.840 Da / Num. of mol.: 6 / 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.: 11 / 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 , 5 types, 189 molecules

#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 172 / 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: 3.46 Å3/Da / Density % sol: 64.5 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 12% isopropanol, 0.2 M calcium acetate, 0.1 M MES, 0.1 M LiCl, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Components of the solutions
IDNameCrystal-IDSol-ID
1isopropanol11
2calcium acetate11
3MES11
4LiCl11
5isopropanol12
6calcium acetate12
7MES12
8LiCl12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.9793 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 11, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3.2→30 Å / Num. all: 54218 / Num. obs: 50322 / % possible obs: 92.8 % / Rmerge(I) obs: 0.139 / Net I/σ(I): 14.7
Reflection shellResolution: 3.2→3.3 Å / Rmerge(I) obs: 0.417 / Mean I/σ(I) obs: 3.2

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Processing

Software
NameVersionClassification
PHASERphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2KQ9

2kq9


Resolution: 3.2→30 Å / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2685 1752 -random
Rwork0.2122 ---
all-54218 --
obs-50322 92.8 %-
Displacement parametersBiso mean: 62.4 Å2
Refinement stepCycle: LAST / Resolution: 3.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12641 3393 35 172 16241
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007383
X-RAY DIFFRACTIONc_angle_deg1.47097
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_mcbond_it1.3251.5
X-RAY DIFFRACTIONc_mcangle_it2.3922
X-RAY DIFFRACTIONc_scbond_it1.552
X-RAY DIFFRACTIONc_scangle_it2.5542.5

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