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- PDB-5use: 5-Se-T4-DNA and native RNA hybrid in complex with RNase H catalyt... -

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Basic information

Entry
Database: PDB / ID: 5use
Title5-Se-T4-DNA and native RNA hybrid in complex with RNase H catalytic domain D132N mutant
Components
  • DNA (5'-D(*AP*TP*GP*(T5S)P*CP*G)-3')
  • RNA (5'-R(*UP*CP*GP*AP*CP*A)-3')
  • Ribonuclease H
KeywordsHYDROLASE / RNA / DNA / HYDROLASE - RNA - 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 / RNA / Ribonuclease H
Similarity search - Component
Biological speciesBacillus halodurans (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 Å
AuthorsFang, Z. / Qin, L. / Huang, Z.
CitationJournal: Chemistryselect / Year: 2023
Title: Synthesis of Pyrimidine Modified Seleno-DNA as a Novel Approach to Antisense Candidate
Authors: Fang, Z. / Dantsu, Y. / Chen, C. / Zhang, W. / Huang, Z.
History
DepositionFeb 13, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 8, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 2, 2023Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _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.ptnr1_symmetry / _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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _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.ptnr1_symmetry / _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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id
Revision 1.2Oct 4, 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
B: RNA (5'-R(*UP*CP*GP*AP*CP*A)-3')
C: DNA (5'-D(*AP*TP*GP*(T5S)P*CP*G)-3')
A: Ribonuclease H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1565
Polymers20,1083
Non-polymers492
Water57632
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2020 Å2
ΔGint-24 kcal/mol
Surface area8600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.912, 37.560, 62.258
Angle α, β, γ (deg.)90.00, 96.17, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: RNA chain RNA (5'-R(*UP*CP*GP*AP*CP*A)-3')


Mass: 1875.189 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(*AP*TP*GP*(T5S)P*CP*G)-3')


Mass: 1903.188 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Protein Ribonuclease H / RNase H


Mass: 16329.478 Da / Num. of mol.: 1 / Fragment: residues 59-196 / 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 K-12 (bacteria) / References: UniProt: Q9KEI9, ribonuclease H
#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.: 32 / 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: 2.35 Å3/Da / Density % sol: 47.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1M MES pH 6.5, 12%(w/v) PEG 20000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.73→50 Å / Num. obs: 19601 / % possible obs: 99.8 % / Redundancy: 6 % / Rpim(I) all: 0.039 / Net I/σ(I): 53.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2g8u

2g8u


Resolution: 1.73→30.949 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.943 / SU B: 2.224 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R: 0.109 / ESU R Free: 0.112 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23398 1034 5.3 %RANDOM
Rwork0.19196 ---
obs0.19419 18567 99.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.801 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å2-0 Å20 Å2
2---0.01 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.73→30.949 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1076 246 2 32 1356
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0181373
X-RAY DIFFRACTIONr_bond_other_d0.0150.021181
X-RAY DIFFRACTIONr_angle_refined_deg2.0391.8131905
X-RAY DIFFRACTIONr_angle_other_deg1.2453.0052740
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3845131
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.08225.09851
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.09915202
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.317155
X-RAY DIFFRACTIONr_chiral_restr0.1320.2205
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021354
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02299
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.6142.481527
X-RAY DIFFRACTIONr_mcbond_other2.5842.477526
X-RAY DIFFRACTIONr_mcangle_it3.4923.701657
X-RAY DIFFRACTIONr_mcangle_other3.4933.705658
X-RAY DIFFRACTIONr_scbond_it3.6792.906846
X-RAY DIFFRACTIONr_scbond_other3.6772.907847
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.294.2351249
X-RAY DIFFRACTIONr_long_range_B_refined6.40622.3541673
X-RAY DIFFRACTIONr_long_range_B_other6.40922.2951663
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.73→1.775 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 79 -
Rwork0.218 1344 -
obs--98 %

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