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- PDB-4opk: Bh-RNaseH:2'-SMe-DNA complex -

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Basic information

Entry
Database: PDB / ID: 4opk
TitleBh-RNaseH:2'-SMe-DNA complex
Components
  • 5'-D(*CP*GP*CP*GP*AP*AP*(USM)P*TP*CP*GP*CP*G)-3'
  • Ribonuclease H
KeywordsHYDROLASE/DNA / Bh RNase-H:DNA complex / protein-DNA complex / RNase H / Ribonuclease H / 2'thiomethyl DNA / HYDROLASE-DNA complex
Function / homology
Function and homology information


ribonuclease H / RNA-DNA hybrid ribonuclease activity / nucleic acid binding / metal ion binding / cytoplasm
Similarity search - Function
Ribonuclease H, Bacteroides-type / Ribonuclease H1, N-terminal / Ribonuclease H1, N-terminal domain superfamily / Caulimovirus viroplasmin / Ribonuclease H-like superfamily/Ribonuclease H / Ribosomal protein L9/RNase H1, N-terminal / RNase H type-1 domain profile. / Ribonuclease H domain / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily ...Ribonuclease H, Bacteroides-type / Ribonuclease H1, N-terminal / Ribonuclease H1, N-terminal domain superfamily / Caulimovirus viroplasmin / Ribonuclease H-like superfamily/Ribonuclease H / Ribosomal protein L9/RNase H1, N-terminal / 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) / Ribonuclease H
Similarity search - Component
Biological speciesBacillus halodurans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.539 Å
AuthorsPallan, P.S. / Egli, M.
CitationJournal: Methods Mol.Biol.
Title: Generating Crystallographic Models of DNA Dodecamers from Structures of RNase H:DNA Complexes.
Authors: Egli, M. / Pallan, P.S.
History
DepositionFeb 5, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 11, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 12, 2015Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribonuclease H
B: 5'-D(*CP*GP*CP*GP*AP*AP*(USM)P*TP*CP*GP*CP*G)-3'
C: Ribonuclease H
D: 5'-D(*CP*GP*CP*GP*AP*AP*(USM)P*TP*CP*GP*CP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2346
Polymers40,0504
Non-polymers1842
Water3,531196
1
B: 5'-D(*CP*GP*CP*GP*AP*AP*(USM)P*TP*CP*GP*CP*G)-3'

A: Ribonuclease H
B: 5'-D(*CP*GP*CP*GP*AP*AP*(USM)P*TP*CP*GP*CP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8124
Polymers23,7203
Non-polymers921
Water543
TypeNameSymmetry operationNumber
crystal symmetry operation2_555-x,y,-z1
identity operation1_555x,y,z1
2
D: 5'-D(*CP*GP*CP*GP*AP*AP*(USM)P*TP*CP*GP*CP*G)-3'

C: Ribonuclease H
D: 5'-D(*CP*GP*CP*GP*AP*AP*(USM)P*TP*CP*GP*CP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8124
Polymers23,7203
Non-polymers921
Water543
TypeNameSymmetry operationNumber
crystal symmetry operation2_656-x+1,y,-z+11
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)98.138, 66.609, 77.898
Angle α, β, γ (deg.)90.00, 122.05, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Ribonuclease H / RNase H


Mass: 16329.478 Da / Num. of mol.: 2 / Fragment: UNP residues 59-196 / Mutation: D132N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus halodurans (bacteria) / Gene: BH0863, rnhA / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9KEI9, ribonuclease H
#2: DNA chain 5'-D(*CP*GP*CP*GP*AP*AP*(USM)P*TP*CP*GP*CP*G)-3'


Mass: 3695.457 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: 2'-SMe-uridine DNA
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 196 / 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: 2.69 Å3/Da / Density % sol: 54.34 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.1 M sodium acetate, 8% w/v PEG4000, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 21, 2007
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.539→66.024 Å / Num. all: 59362 / Num. obs: 59362 / % possible obs: 94.2 % / Observed criterion σ(I): 5 / Redundancy: 2.4 % / Rmerge(I) obs: 0.047 / Net I/σ(I): 28.3
Reflection shellResolution: 1.539→1.57 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.675 / Mean I/σ(I) obs: 1.27 / Num. unique all: 2885 / % possible all: 91.8

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Processing

Software
NameVersionClassification
MD2diffractometer software from EMBL (with LS-CAT developed extensions)data collection
MOLREPphasing
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3D0P

3d0p


Resolution: 1.539→66.02 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.941 / SU B: 5.019 / SU ML: 0.076 / Cross valid method: THROUGHOUT / σ(I): 5 / ESU R: 0.099 / ESU R Free: 0.096 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2582 4611 7.8 %RANDOM
Rwork0.1939 ---
obs0.19893 54674 93.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.586 Å2
Baniso -1Baniso -2Baniso -3
1--0.73 Å2-0 Å2-0.74 Å2
2---0.78 Å20 Å2
3---1.36 Å2
Refinement stepCycle: LAST / Resolution: 1.539→66.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2156 488 12 196 2852
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0182800
X-RAY DIFFRACTIONr_angle_refined_deg2.3241.8373896
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0365268
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.02825.238105
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.0115414
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.5281510
X-RAY DIFFRACTIONr_chiral_restr0.1960.2410
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.0211920
X-RAY DIFFRACTIONr_mcbond_it4.912.8171065
X-RAY DIFFRACTIONr_mcangle_it5.3614.2151331
X-RAY DIFFRACTIONr_scbond_it6.3043.3341735
X-RAY DIFFRACTIONr_rigid_bond_restr10.0632800
X-RAY DIFFRACTIONr_sphericity_free27.589592
X-RAY DIFFRACTIONr_sphericity_bonded19.48852796
LS refinement shellResolution: 1.539→1.579 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.348 314 -
Rwork0.349 3920 -
obs--90.66 %

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