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- PDB-3d0p: Insights into RNA/DNA hybrid recognition and processing by RNase ... -

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Basic information

Entry
Database: PDB / ID: 3d0p
TitleInsights into RNA/DNA hybrid recognition and processing by RNase H from the crystal structure of a non-specific enzyme-dsDNA complex
Components
  • DNA (5'-D(*DCP*DGP*DCP*DGP*DAP*DAP*DTP*DTP*DCP*DGP*DCP*DG)-3')
  • Ribonuclease H
Keywordshydrolase/DNA / RNase H-DNA complex / A-form / B-form / metal ions / protein-DNA complex / Cytoplasm / Endonuclease / Hydrolase / Magnesium / Manganese / Metal-binding / Nuclease / 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
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsPallan, P.S. / Egli, M.
CitationJournal: Cell Cycle / Year: 2008
Title: Insights into RNA/DNA hybrid recognition and processing by RNase H from the crystal structure of a non-specific enzyme-dsDNA complex.
Authors: Pallan, P.S. / Egli, M.
History
DepositionMay 2, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Aug 30, 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
A: Ribonuclease H
B: DNA (5'-D(*DCP*DGP*DCP*DGP*DAP*DAP*DTP*DTP*DCP*DGP*DCP*DG)-3')
C: Ribonuclease H
D: DNA (5'-D(*DCP*DGP*DCP*DGP*DAP*DAP*DTP*DTP*DCP*DGP*DCP*DG)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,2095
Polymers38,1864
Non-polymers231
Water2,990166
1
A: Ribonuclease H
B: DNA (5'-D(*DCP*DGP*DCP*DGP*DAP*DAP*DTP*DTP*DCP*DGP*DCP*DG)-3')

A: Ribonuclease H
B: DNA (5'-D(*DCP*DGP*DCP*DGP*DAP*DAP*DTP*DTP*DCP*DGP*DCP*DG)-3')


Theoretical massNumber of molelcules
Total (without water)38,1864
Polymers38,1864
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area4040 Å2
ΔGint-19 kcal/mol
Surface area15980 Å2
MethodPISA
2
C: Ribonuclease H
D: DNA (5'-D(*DCP*DGP*DCP*DGP*DAP*DAP*DTP*DTP*DCP*DGP*DCP*DG)-3')
hetero molecules

C: Ribonuclease H
D: DNA (5'-D(*DCP*DGP*DCP*DGP*DAP*DAP*DTP*DTP*DCP*DGP*DCP*DG)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,2326
Polymers38,1864
Non-polymers462
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area4400 Å2
ΔGint-38 kcal/mol
Surface area16050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.397, 66.660, 76.926
Angle α, β, γ (deg.)90.00, 122.31, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe second part of the biological assembly is generated by the two fold axis of Chain identifier A: -X, Y, -Z -1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 -1.000000 / The second part of the biological assembly is generated by the two fold axis of Chain identifier B: -X, Y, -Z -1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 -1.000000

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Components

#1: Protein Ribonuclease H / RNase H


Mass: 15429.371 Da / Num. of mol.: 2 / Mutation: D132N / Source method: obtained synthetically / Details: Bacillus halodurans RNase H, D132N mutant / References: UniProt: Q9KEI9, ribonuclease H
#2: DNA chain DNA (5'-D(*DCP*DGP*DCP*DGP*DAP*DAP*DTP*DTP*DCP*DGP*DCP*DG)-3')


Mass: 3663.392 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Synthetic DNA
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 166 / 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: 2.79 Å3/Da / Density % sol: 55.94 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.1 M sodium acetate, 8 % (w/v) PEG 4000, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Components of the solutions
IDNameCrystal-IDSol-ID
1sodium acetate11
2PEG 400011
3sodium acetate12
4PEG 400012

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9785 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 21, 2007
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 38816 / Num. obs: 37768 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.7 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 12.4
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.248 / Mean I/σ(I) obs: 12.4 / Num. unique all: 3643 / % possible all: 94.7

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Processing

Software
NameVersionClassification
REFMAC5.4.0066refinement
MAR345dtbdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ZBI, using one protein molecule.

1zbi


Resolution: 1.8→41.59 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.951 / SU B: 5.491 / SU ML: 0.086 / Cross valid method: THROUGHOUT / ESU R: 0.133 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24108 1886 5 %RANDOM
Rwork0.21396 ---
obs0.21539 35877 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.474 Å2
Baniso -1Baniso -2Baniso -3
1--1.44 Å20 Å2-1.42 Å2
2---1.4 Å20 Å2
3---1.32 Å2
Refinement stepCycle: LAST / Resolution: 1.8→41.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2169 486 1 166 2822
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222763
X-RAY DIFFRACTIONr_angle_refined_deg1.6722.1753844
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9255265
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.55825.146103
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.62715406
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2741510
X-RAY DIFFRACTIONr_chiral_restr0.120.2421
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211906
X-RAY DIFFRACTIONr_mcbond_it1.0421.51323
X-RAY DIFFRACTIONr_mcangle_it1.86222148
X-RAY DIFFRACTIONr_scbond_it2.44831440
X-RAY DIFFRACTIONr_scangle_it3.6334.51696
LS refinement shellResolution: 1.803→1.849 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 120 -
Rwork0.256 2515 -
obs-2515 100 %
Refinement TLS params.Method: refined / Origin x: 32.4421 Å / Origin y: 1.845 Å / Origin z: 18.6056 Å
111213212223313233
T-0.0111 Å2-0.0155 Å2-0.0067 Å2--0.0474 Å20.0369 Å2---0.0271 Å2
L0.7634 °20.1292 °20.6812 °2-0.0489 °20.0981 °2--0.6241 °2
S-0.0048 Å °0.079 Å °0.0547 Å °0.032 Å °-0.0239 Å °0.0141 Å °0.0094 Å °0.1036 Å °0.0286 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA61 - 1941 - 134
2X-RAY DIFFRACTION1BB1 - 121 - 12
3X-RAY DIFFRACTION1CC62 - 1942 - 134
4X-RAY DIFFRACTION1DD1 - 121 - 12

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