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

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Basic information

Entry
Database: PDB / ID: 4htu
TitleStructure of 5-chlorouracil modified A:U base pair
Components
  • DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*(UCL)P*CP*GP*CP*G)-3')
  • Ribonuclease H
KeywordsHydrolase/DNA / 5-chloro-2'-deoxyuridine / W-C base pair / wobble base pair / double helix / 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: 1.489 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 1, 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*TP*(UCL)P*CP*GP*CP*G)-3')
D: DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*(UCL)P*CP*GP*CP*G)-3')
E: DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*(UCL)P*CP*GP*CP*G)-3')
F: DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*(UCL)P*CP*GP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,98112
Polymers45,5946
Non-polymers3876
Water8,665481
1
A: Ribonuclease H
C: DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*(UCL)P*CP*GP*CP*G)-3')
D: DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*(UCL)P*CP*GP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9135
Polymers22,7973
Non-polymers1162
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ribonuclease H
E: DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*(UCL)P*CP*GP*CP*G)-3')
F: DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*(UCL)P*CP*GP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0687
Polymers22,7973
Non-polymers2714
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.075, 64.756, 116.469
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
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*(UCL)P*CP*GP*CP*G)-3')


Mass: 3683.811 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: ClU8

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Non-polymers , 4 types, 487 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.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 481 / 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: 53.58 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting 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, 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 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: 1.489→58.235 Å / Num. all: 80004 / Num. obs: 77452 / % possible obs: 96.9 % / Observed criterion σ(I): -3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allDiffraction-ID% possible all
1.49-1.526.40.8313700195.1
1.52-1.546.70.7223742195
1.54-1.576.70.63761195.6

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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: 1.489→35.877 Å / SU ML: 0.14 / σ(F): 5 / Phase error: 22.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2181 3759 5.03 %RANDOM
Rwork0.1888 ---
obs0.2181 74662 93.4 %-
all-77123 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.489→35.877 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2178 833 24 481 3516
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083339
X-RAY DIFFRACTIONf_angle_d1.3044729
X-RAY DIFFRACTIONf_dihedral_angle_d25.3581324
X-RAY DIFFRACTIONf_chiral_restr0.075508
X-RAY DIFFRACTIONf_plane_restr0.005445
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4893-1.50820.2751400.25032225X-RAY DIFFRACTION81
1.5082-1.5280.27071180.24312343X-RAY DIFFRACTION84
1.528-1.5490.27941320.24252364X-RAY DIFFRACTION85
1.549-1.57110.25261250.22792406X-RAY DIFFRACTION86
1.5711-1.59450.22211000.21832434X-RAY DIFFRACTION87
1.5945-1.61950.22731150.2352507X-RAY DIFFRACTION90
1.6195-1.6460.2811190.21762493X-RAY DIFFRACTION89
1.646-1.67440.23331330.21462487X-RAY DIFFRACTION91
1.6744-1.70480.25321280.21332595X-RAY DIFFRACTION92
1.7048-1.73760.26461280.20792552X-RAY DIFFRACTION92
1.7376-1.77310.2761470.20512595X-RAY DIFFRACTION93
1.7731-1.81160.25971310.20562611X-RAY DIFFRACTION94
1.8116-1.85380.25971410.21072646X-RAY DIFFRACTION94
1.8538-1.90010.24881230.20512661X-RAY DIFFRACTION95
1.9001-1.95150.25131480.2012657X-RAY DIFFRACTION95
1.9515-2.00890.24791440.20022661X-RAY DIFFRACTION96
2.0089-2.07380.22911440.18692718X-RAY DIFFRACTION96
2.0738-2.14790.21681610.1812700X-RAY DIFFRACTION97
2.1479-2.23390.20381420.17632733X-RAY DIFFRACTION97
2.2339-2.33550.2171530.17682740X-RAY DIFFRACTION97
2.3355-2.45860.18371610.17542719X-RAY DIFFRACTION97
2.4586-2.61260.20631710.19082757X-RAY DIFFRACTION98
2.6126-2.81430.24831660.19242764X-RAY DIFFRACTION98
2.8143-3.09730.22341410.19222823X-RAY DIFFRACTION99
3.0973-3.54520.21151450.18482836X-RAY DIFFRACTION99
3.5452-4.46520.16881530.15952878X-RAY DIFFRACTION99
4.4652-35.88710.2051500.18322998X-RAY DIFFRACTION98

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