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- PDB-4hue: Structure of 5-chlorouracil modified G:U base pair -

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Basic information

Entry
Database: PDB / ID: 4hue
TitleStructure of 5-chlorouracil modified G:U base pair
Components
  • DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*(UCL)P*GP*CP*G)-3')
  • Ribonuclease H
KeywordsHydrolase/DNA / 5-chloro-2'-deoxyuridine / W-C base pair / wobble base pair / double helix / Wobble Base pairing pattern / Hydrolase-DNA complex
Function / homology
Function and homology information


DNA replication, removal of RNA primer / 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 / Ribonuclease H1 N-terminal domain / : / 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, Bacteroides-type / 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 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: 1.561 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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*TP*TP*(UCL)P*GP*CP*G)-3')
D: DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*(UCL)P*GP*CP*G)-3')
E: DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*(UCL)P*GP*CP*G)-3')
F: DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*(UCL)P*GP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,07112
Polymers45,6546
Non-polymers4176
Water8,233457
1
A: Ribonuclease H
C: DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*(UCL)P*GP*CP*G)-3')
D: DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*(UCL)P*GP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1287
Polymers22,8273
Non-polymers3014
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3780 Å2
ΔGint-15 kcal/mol
Surface area10490 Å2
MethodPISA
2
B: Ribonuclease H
E: DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*(UCL)P*GP*CP*G)-3')
F: DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*(UCL)P*GP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9435
Polymers22,8273
Non-polymers1162
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2750 Å2
ΔGint-17 kcal/mol
Surface area9510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.360, 64.808, 116.622
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#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*TP*TP*(UCL)P*GP*CP*G)-3')


Mass: 3698.822 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: Dickerson Dodecamer DNA, ClU9
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 457 / 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: 2.66 Å3/Da / Density % sol: 53.82 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / 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-D / Wavelength: 0.9793 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 4, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.56→50 Å / Num. all: 68234 / Num. obs: 68193 / % possible obs: 97.3 % / Observed criterion σ(I): -3 / Redundancy: 6.2 %
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.56-1.596.10.8196.6
1.59-1.626.20.659196.5
1.62-1.656.20.545196.9

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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: 1.561→33.275 Å / SU ML: 0.15 / σ(F): 1.34 / Phase error: 22.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2201 3453 5.07 %
Rwork0.1921 --
obs0.1936 68154 97.25 %
all-68234 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.561→33.275 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2168 814 26 457 3465
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083201
X-RAY DIFFRACTIONf_angle_d1.2294520
X-RAY DIFFRACTIONf_dihedral_angle_d23.0161249
X-RAY DIFFRACTIONf_chiral_restr0.069488
X-RAY DIFFRACTIONf_plane_restr0.005429
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5605-1.58190.2441170.27012480X-RAY DIFFRACTION94
1.5819-1.60450.30731450.2452535X-RAY DIFFRACTION97
1.6045-1.62850.30021570.24912522X-RAY DIFFRACTION97
1.6285-1.65390.2381350.23672519X-RAY DIFFRACTION96
1.6539-1.6810.28661450.22972526X-RAY DIFFRACTION97
1.681-1.710.25741240.22812570X-RAY DIFFRACTION97
1.71-1.74110.23721380.21612553X-RAY DIFFRACTION97
1.7411-1.77460.26311330.21482561X-RAY DIFFRACTION98
1.7746-1.81080.23961390.2132583X-RAY DIFFRACTION98
1.8108-1.85020.22571140.20462614X-RAY DIFFRACTION98
1.8502-1.89320.25971050.20272596X-RAY DIFFRACTION97
1.8932-1.94060.21431210.19742592X-RAY DIFFRACTION98
1.9406-1.9930.21891540.19892584X-RAY DIFFRACTION98
1.993-2.05170.23941410.19342606X-RAY DIFFRACTION98
2.0517-2.11790.21541610.18522591X-RAY DIFFRACTION98
2.1179-2.19350.18011300.19252596X-RAY DIFFRACTION98
2.1935-2.28140.21391460.182627X-RAY DIFFRACTION98
2.2814-2.38520.21461370.18762628X-RAY DIFFRACTION98
2.3852-2.51090.22491390.19372618X-RAY DIFFRACTION99
2.5109-2.66810.23131310.1962661X-RAY DIFFRACTION99
2.6681-2.8740.21381610.19492603X-RAY DIFFRACTION99
2.874-3.1630.21891420.19322653X-RAY DIFFRACTION98
3.163-3.62030.20161400.17492650X-RAY DIFFRACTION97
3.6203-4.55930.19491490.16062629X-RAY DIFFRACTION97
4.5593-33.28270.23451490.20392604X-RAY DIFFRACTION91

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