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- PDB-4hug: Structure of 5-chlorouracil modified A:U base pairs -

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Basic information

Entry
Database: PDB / ID: 4hug
TitleStructure of 5-chlorouracil modified A:U base pairs
Components
  • DNA (5'-D(*CP*GP*CP*GP*AP*AP*(UCL)P*(UCL)P*CP*GP*CP*G)-3')
  • Ribonuclease H
KeywordsHydrolase/DNA / 5-chloro-2'-deoxyuridine / W-C base pair / Wobble base pair / double helix / Watson-Crick base pairing pattern / 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: 1.64 Å
AuthorsPatra, A. / Egli, M.
CitationJournal: Nucleic Acids Res. / Year: 2013
Title: Structure, stability and function of 5-chlorouracil modified A:U and G:U base pairs.
Authors: Patra, A. / Harp, J. / Pallan, P.S. / Zhao, L. / Abramov, M. / Herdewijn, P. / Egli, M.
History
DepositionNov 2, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 19, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 13, 2013Group: Database references
Revision 1.2Mar 27, 2013Group: Database references
Revision 1.3Sep 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 / 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.pdbx_leaving_atom_flag / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribonuclease H
B: Ribonuclease H
C: DNA (5'-D(*CP*GP*CP*GP*AP*AP*(UCL)P*(UCL)P*CP*GP*CP*G)-3')
D: DNA (5'-D(*CP*GP*CP*GP*AP*AP*(UCL)P*(UCL)P*CP*GP*CP*G)-3')
E: DNA (5'-D(*CP*GP*CP*GP*AP*AP*(UCL)P*(UCL)P*CP*GP*CP*G)-3')
F: DNA (5'-D(*CP*GP*CP*GP*AP*AP*(UCL)P*(UCL)P*CP*GP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,03312
Polymers45,6766
Non-polymers3576
Water7,710428
1
A: Ribonuclease H
C: DNA (5'-D(*CP*GP*CP*GP*AP*AP*(UCL)P*(UCL)P*CP*GP*CP*G)-3')
D: DNA (5'-D(*CP*GP*CP*GP*AP*AP*(UCL)P*(UCL)P*CP*GP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9545
Polymers22,8383
Non-polymers1162
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ribonuclease H
E: DNA (5'-D(*CP*GP*CP*GP*AP*AP*(UCL)P*(UCL)P*CP*GP*CP*G)-3')
F: DNA (5'-D(*CP*GP*CP*GP*AP*AP*(UCL)P*(UCL)P*CP*GP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0787
Polymers22,8383
Non-polymers2414
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.829, 64.638, 116.286
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / DNA chain , 2 types, 6 molecules ABCDEF

#1: Protein Ribonuclease H / RNase H


Mass: 15429.371 Da / Num. of mol.: 2 / Mutation: D132N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus halodurans (bacteria)
Strain: ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125
Gene: rnhA, BH0863 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9KEI9, ribonuclease H
#2: DNA chain
DNA (5'-D(*CP*GP*CP*GP*AP*AP*(UCL)P*(UCL)P*CP*GP*CP*G)-3')


Mass: 3704.230 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: Dickerson Dodecamer DNA, ClU7/8

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Non-polymers , 4 types, 434 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#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.: 428 / 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: 2.63 Å3/Da / Density % sol: 53.16 %
Crystal growTemperature: 277 K / pH: 6.5
Details: 0.2 M magnesium acetate, 0.1 M sodium cacodylate and 20% (w/v) PEG 8000 , pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 11, 2011
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.64→50 Å / Num. obs: 59379 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 8.5 %
Reflection shellResolution: 1.64→1.67 Å / Rmerge(I) obs: 0.674 / % possible all: 99.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3D0P

3d0p


Resolution: 1.64→43.228 Å / SU ML: 0.16 / Isotropic thermal model: Isotropic / σ(F): 1.35 / Phase error: 20.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2218 2996 5.05 %
Rwork0.1931 --
obs0.1945 59371 99.56 %
all-59446 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.64→43.228 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2154 833 22 428 3437
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083234
X-RAY DIFFRACTIONf_angle_d1.3194571
X-RAY DIFFRACTIONf_dihedral_angle_d26.1911288
X-RAY DIFFRACTIONf_chiral_restr0.078489
X-RAY DIFFRACTIONf_plane_restr0.005435
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6405-1.66740.2921210.25582549X-RAY DIFFRACTION96
1.6674-1.69610.29531590.23072636X-RAY DIFFRACTION99
1.6961-1.72690.22661290.22752634X-RAY DIFFRACTION99
1.7269-1.76020.27631400.2272646X-RAY DIFFRACTION100
1.7602-1.79610.22251590.21942644X-RAY DIFFRACTION99
1.7961-1.83510.24461320.21872644X-RAY DIFFRACTION99
1.8351-1.87780.26151350.21112681X-RAY DIFFRACTION100
1.8778-1.92480.2681400.20242662X-RAY DIFFRACTION100
1.9248-1.97680.22891530.19582659X-RAY DIFFRACTION100
1.9768-2.0350.20941550.18562630X-RAY DIFFRACTION100
2.035-2.10070.19421450.17612681X-RAY DIFFRACTION100
2.1007-2.17580.20451390.17992690X-RAY DIFFRACTION100
2.1758-2.26290.20021320.17632685X-RAY DIFFRACTION100
2.2629-2.36590.21221370.18432693X-RAY DIFFRACTION100
2.3659-2.49060.20091610.18792679X-RAY DIFFRACTION100
2.4906-2.64660.19341400.18852701X-RAY DIFFRACTION100
2.6466-2.85090.19861460.19382711X-RAY DIFFRACTION100
2.8509-3.13770.21871350.19972741X-RAY DIFFRACTION100
3.1377-3.59160.2611470.18982744X-RAY DIFFRACTION100
3.5916-4.52430.20661360.17142772X-RAY DIFFRACTION100
4.5243-43.24270.22291550.20532893X-RAY DIFFRACTION99

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