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- PDB-4huf: Structure of 5-chlorouracil modified A:U base pair -

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Basic information

Entry
Database: PDB / ID: 4huf
TitleStructure of 5-chlorouracil modified A:U base pair
Components
  • DNA (5'-D(*CP*GP*CP*GP*AP*AP*(UCL)P*TP*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


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: 1.69 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 1.3Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4Sep 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*(UCL)P*TP*CP*GP*CP*G)-3')
D: DNA (5'-D(*CP*GP*CP*GP*AP*AP*(UCL)P*TP*CP*GP*CP*G)-3')
E: DNA (5'-D(*CP*GP*CP*GP*AP*AP*(UCL)P*TP*CP*GP*CP*G)-3')
F: DNA (5'-D(*CP*GP*CP*GP*AP*AP*(UCL)P*TP*CP*GP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,95112
Polymers45,5946
Non-polymers3576
Water8,107450
1
A: Ribonuclease H
C: DNA (5'-D(*CP*GP*CP*GP*AP*AP*(UCL)P*TP*CP*GP*CP*G)-3')
D: DNA (5'-D(*CP*GP*CP*GP*AP*AP*(UCL)P*TP*CP*GP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0056
Polymers22,7973
Non-polymers2083
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ribonuclease H
E: DNA (5'-D(*CP*GP*CP*GP*AP*AP*(UCL)P*TP*CP*GP*CP*G)-3')
F: DNA (5'-D(*CP*GP*CP*GP*AP*AP*(UCL)P*TP*CP*GP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9456
Polymers22,7973
Non-polymers1483
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.193, 64.748, 116.470
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: BH0863, rnhA / 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*TP*CP*GP*CP*G)-3')


Mass: 3683.811 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: Dickerson Dodecamer DNA, ClU7

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Non-polymers , 4 types, 456 molecules

#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: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#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.: 450 / 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: 2.65 Å3/Da / Density % sol: 53.66 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2 M magnesium acetate, 0.1 M sodium cacodylate (pH 6.5) and 20% (w/v) PEG 8000 , VAPOR DIFFUSION, HANGING 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 Å
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: 1.69→50 Å / Num. all: 54372 / Num. obs: 54315 / % possible obs: 98.3 % / Observed criterion σ(I): -3 / Redundancy: 7.4 %
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allDiffraction-ID% possible all
1.69-1.727.10.6752620197.3
1.72-1.757.10.5612669197.3
1.75-1.787.20.4812632196.8

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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: 1.69→35.896 Å / SU ML: 0.17 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 5 / Phase error: 21.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2277 2766 5.09 %RANDOM
Rwork0.1919 ---
obs0.2277 54302 98.23 %-
all-54372 --
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.69→35.896 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2151 833 22 450 3456
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083208
X-RAY DIFFRACTIONf_angle_d1.3294533
X-RAY DIFFRACTIONf_dihedral_angle_d25.9671261
X-RAY DIFFRACTIONf_chiral_restr0.08490
X-RAY DIFFRACTIONf_plane_restr0.005429
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6881-1.71720.29931240.24372460X-RAY DIFFRACTION95
1.7172-1.74850.28021680.23772484X-RAY DIFFRACTION97
1.7485-1.78210.25551450.22772497X-RAY DIFFRACTION97
1.7821-1.81850.28331410.22182510X-RAY DIFFRACTION98
1.8185-1.8580.25481210.2132542X-RAY DIFFRACTION98
1.858-1.90120.23581420.20362546X-RAY DIFFRACTION98
1.9012-1.94880.21141420.19482513X-RAY DIFFRACTION97
1.9488-2.00150.26731400.19432530X-RAY DIFFRACTION98
2.0015-2.06040.20431250.17682553X-RAY DIFFRACTION98
2.0604-2.12680.21871360.17522571X-RAY DIFFRACTION98
2.1268-2.20290.21131540.17972543X-RAY DIFFRACTION98
2.2029-2.2910.22741220.17332601X-RAY DIFFRACTION98
2.291-2.39530.23181340.18422576X-RAY DIFFRACTION99
2.3953-2.52150.23881280.19442611X-RAY DIFFRACTION99
2.5215-2.67950.23821630.19872586X-RAY DIFFRACTION99
2.6795-2.88630.23981330.19822615X-RAY DIFFRACTION100
2.8863-3.17660.28431170.20462646X-RAY DIFFRACTION99
3.1766-3.63590.20951470.18532651X-RAY DIFFRACTION99
3.6359-4.57930.19251410.16932698X-RAY DIFFRACTION100
4.5793-35.90420.21141430.20062803X-RAY DIFFRACTION99

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