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- PDB-5vaj: BhRNase H - amide-RNA/DNA complex -

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Basic information

Entry
Database: PDB / ID: 5vaj
TitleBhRNase H - amide-RNA/DNA complex
Components
  • DNA (5'-D(*GP*AP*AP*TP*CP*AP*GP*GP*TP*GP*TP*C)-3')
  • RNA (5'-R(*GP*AP*CP*AP*CP*CP*UP*GP*AP*(URU)P*C)-3')
  • Ribonuclease H
Keywordshydrolase/rna/dna / Amide-RNA / siRNA / RNA X-ray structure / phosphate modification / RIBONUCLEASE H / amide modified RNA-DNA. / hydrolase-rna-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
ACETATE ION / DNA / DNA (> 10) / RNA / RNA (> 10) / Ribonuclease H
Similarity search - Component
Biological speciesBacillus halodurans (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsPallan, P.S. / Egli, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM71461 United States
CitationJournal: Nucleic Acids Res. / Year: 2017
Title: Amide linkages mimic phosphates in RNA interactions with proteins and are well tolerated in the guide strand of short interfering RNAs.
Authors: Mutisya, D. / Hardcastle, T. / Cheruiyot, S.K. / Pallan, P.S. / Kennedy, S.D. / Egli, M. / Kelley, M.L. / Smith, A.V.B. / Rozners, E.
History
DepositionMar 27, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 13, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 4, 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 / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: RNA (5'-R(*GP*AP*CP*AP*CP*CP*UP*GP*AP*(URU)P*C)-3')
D: DNA (5'-D(*GP*AP*AP*TP*CP*AP*GP*GP*TP*GP*TP*C)-3')
A: Ribonuclease H
B: Ribonuclease H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,19820
Polymers40,0954
Non-polymers1,10316
Water3,855214
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7680 Å2
ΔGint-73 kcal/mol
Surface area16130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.180, 37.513, 93.863
Angle α, β, γ (deg.)90.00, 121.65, 90.00
Int Tables number5
Space group name H-MC121

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Components

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RNA chain / DNA chain / Protein , 3 types, 4 molecules CDAB

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


Mass: 3733.368 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(*GP*AP*AP*TP*CP*AP*GP*GP*TP*GP*TP*C)-3')


Mass: 3702.428 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.: 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 / Variant: D132N / Plasmid: pET15b / Cell (production host): BL21 / Production host: Escherichia coli (E. coli) / Strain (production host): E Coli / References: UniProt: Q9KEI9, ribonuclease H

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Non-polymers , 4 types, 230 molecules

#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 214 / 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: 2.56 Å3/Da / Density % sol: 52.02 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 50 mM sodium cacodylate (pH 6.5) and 0.7 M sodium acetate.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Mar 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.95→80 Å / Num. obs: 30154 / % possible obs: 99.9 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 18.47
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.46 / Num. unique obs: 2958 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ZBI

1zbi


Resolution: 1.95→79.9 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.937 / SU B: 3.194 / SU ML: 0.091 / Cross valid method: THROUGHOUT / ESU R: 0.139 / ESU R Free: 0.139 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21694 1472 4.9 %RANDOM
Rwork0.16564 ---
obs0.16813 28679 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.188 Å2
Baniso -1Baniso -2Baniso -3
1--0.23 Å20 Å2-0.45 Å2
2--0.76 Å2-0 Å2
3---0.01 Å2
Refinement stepCycle: 1 / Resolution: 1.95→79.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2182 494 70 214 2960
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0182866
X-RAY DIFFRACTIONr_bond_other_d0.0030.022425
X-RAY DIFFRACTIONr_angle_refined_deg1.381.8293963
X-RAY DIFFRACTIONr_angle_other_deg1.90535663
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3015269
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.3424.906106
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.02415419
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8271512
X-RAY DIFFRACTIONr_chiral_restr0.150.2424
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.022753
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02560
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_it2.2582.0751085
X-RAY DIFFRACTIONr_mcbond_other2.2232.0631081
X-RAY DIFFRACTIONr_mcangle_it3.2583.0771349
X-RAY DIFFRACTIONr_mcangle_other3.2623.0821350
X-RAY DIFFRACTIONr_scbond_it3.0142.3961781
X-RAY DIFFRACTIONr_scbond_other3.0132.3971782
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.6643.4552615
X-RAY DIFFRACTIONr_long_range_B_refined6.58523.8223443
X-RAY DIFFRACTIONr_long_range_B_other6.48323.5883408
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.949→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 100 -
Rwork0.226 2058 -
obs--98.27 %

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