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- PDB-3i8d: The Pairing Geometry of the Hydrophobic Thymine Analog 2,4-Difluo... -

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Basic information

Entry
Database: PDB / ID: 3i8d
TitleThe Pairing Geometry of the Hydrophobic Thymine Analog 2,4-Difluorotoluene in Duplex DNA as Analyzed by X-ray Crystallography
Components
  • 5'-D(*CP*GP*CP*GP*AP*AP*TP*(DFT)P*CP*GP*CP*G)-3'
  • Ribonuclease H
KeywordsHYDROLASE/DNA / RNase-H / RNase-H DNA-complex / 2 / 4-Difluorotoluene / thymine isostere / hydrophobic base / Endonuclease / Hydrolase / Magnesium / Manganese / Metal-binding / Nuclease / 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 / Ribonuclease H domain / RNase H type-1 domain profile. / 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 / 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) / Ribonuclease H
Similarity search - Component
Biological speciesBacillus halodurans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / using MOLREP / Resolution: 1.61 Å
AuthorsEgli, M. / Pallan, P.S.
CitationJournal: J.Am.Chem.Soc. / Year: 2009
Title: Pairing geometry of the hydrophobic thymine analogue 2,4-difluorotoluene in duplex DNA as analyzed by X-ray crystallography.
Authors: Pallan, P.S. / Egli, M.
History
DepositionJul 9, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 1, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Nov 1, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 1.3Oct 13, 2021Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_unobs_or_zero_occ_atoms ...database_2 / pdbx_unobs_or_zero_occ_atoms / 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 / _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 1.4Sep 6, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)38,1868
Polymers37,8174
Non-polymers3684
Water4,161231
1
A: Ribonuclease H
B: 5'-D(*CP*GP*CP*GP*AP*AP*TP*(DFT)P*CP*GP*CP*G)-3'
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)38,0016
Polymers37,8174
Non-polymers1842
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area5840 Å2
ΔGint-4 kcal/mol
Surface area15820 Å2
MethodPISA
2
C: Ribonuclease H
D: 5'-D(*CP*GP*CP*GP*AP*AP*TP*(DFT)P*CP*GP*CP*G)-3'
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)38,37010
Polymers37,8174
Non-polymers5536
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area6910 Å2
ΔGint-3 kcal/mol
Surface area15580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.178, 66.714, 77.571
Angle α, β, γ (deg.)90.00, 121.04, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe second part of the biological assembly is generated by the two fold axis rotation of chain A and B by: -x, y, -z.

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Components

#1: Protein Ribonuclease H / / RNase H


Mass: 15243.206 Da / Num. of mol.: 2 / Fragment: RNase-H / Mutation: D132N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus halodurans (bacteria)
Gene: BACILLUS HALODURANS, BH0863, RNase-H D132N mutant, rnhA
Production host: Escherichia coli (E. coli) / References: UniProt: Q9KEI9, ribonuclease H
#2: DNA chain 5'-D(*CP*GP*CP*GP*AP*AP*TP*(DFT)P*CP*GP*CP*G)-3'


Mass: 3665.398 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 231 / 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: 2.82 Å3/Da / Density % sol: 56.37 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.1 M NaOAc 3H2O (pH 4.6) and 8% (w/v) PEG 4000 , VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9787 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 17, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 1.61→50 Å / Num. all: 53844 / Num. obs: 52821 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.5 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 39.4
Reflection shellResolution: 1.61→1.64 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 1.7 / Num. measured all: 2686 / Num. unique all: 2203

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Processing

Software
NameVersionClassification
MAR345data collection
MOLREPphasing
REFMAC5.5.0093refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: using MOLREP
Starting model: PDB ID 3D0P

3d0p


Resolution: 1.61→49.39 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.954 / SU B: 4.099 / SU ML: 0.064 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.088 / ESU R Free: 0.094 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: TLS refinement in REFMAC was used
RfactorNum. reflection% reflectionSelection details
Rfree0.23837 2690 5.1 %RANDOM
Rwork0.19721 ---
obs0.19929 50108 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.68 Å2
Baniso -1Baniso -2Baniso -3
1--0.58 Å20 Å2-0.69 Å2
2---0.94 Å20 Å2
3---0.82 Å2
Refinement stepCycle: LAST / Resolution: 1.61→49.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2154 486 24 231 2895
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.030.0222745
X-RAY DIFFRACTIONr_angle_refined_deg2.5362.1813811
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2415262
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.77225.30698
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.63715395
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.398158
X-RAY DIFFRACTIONr_chiral_restr0.1850.2416
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.0211892
X-RAY DIFFRACTIONr_mcbond_it1.4571.51310
X-RAY DIFFRACTIONr_mcangle_it2.35922127
X-RAY DIFFRACTIONr_scbond_it3.42931435
X-RAY DIFFRACTIONr_scangle_it4.6644.51682
LS refinement shellResolution: 1.613→1.655 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.394 158 -
Rwork0.329 2922 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.74610.16830.46283.7545-0.16812.12690.0484-0.0075-0.08310.2655-0.0966-0.0531-0.03710.4430.04820.0566-0.0192-0.01510.15460.04290.020621.2488-1.24382.6758
23.39740.6534-1.07930.1289-0.25651.3937-0.03470.02060.23150.00960.00540.0289-0.20440.01170.02930.1763-0.001-0.04660.04410.00230.18241.13358.58680.088
31.46750.57740.47375.3768-0.11551.0123-0.02680.0692-0.01110.14020.0680.1862-0.00710.0844-0.04120.0310.00560.00460.04230.01640.017449.53752.352436.1506
45.75990.8823-0.86640.1379-0.10540.4733-0.2099-0.05880.2732-0.03740.00060.05570.03690.08530.20930.13250.0015-0.07710.0680.00690.451329.454712.203532.9187
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A62 - 193
2X-RAY DIFFRACTION1A601
3X-RAY DIFFRACTION1A1 - 242
4X-RAY DIFFRACTION2B1 - 12
5X-RAY DIFFRACTION2B13 - 218
6X-RAY DIFFRACTION3C62 - 193
7X-RAY DIFFRACTION3C602 - 604
8X-RAY DIFFRACTION3C14 - 258
9X-RAY DIFFRACTION4D1 - 12
10X-RAY DIFFRACTION4D13 - 232

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