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- PDB-3ey1: A Conformational Transition in the Structure of a 2'-Thiomethyl-M... -

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Basic information

Entry
Database: PDB / ID: 3ey1
TitleA Conformational Transition in the Structure of a 2'-Thiomethyl-Modified DNA Visualized at High Resolution
Components
  • 5'-D(*CP*GP*CP*GP*AP*AP*(USM)P*(USM)P*CP*GP*CP*G)-3'
  • Ribonuclease H
KeywordsHYDROLASE/DNA / RNase H-DNA COMPLEX / PROTEIN-DNA COMPLEX / ENDONUCLEASE / 2'-THIOMETHYL URIDINE RIBONUCLEIC ACID / Hydrolase / Magnesium / Manganese / Metal-binding / Nuclease / 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 / Ribonuclease H domain / RNase H type-1 domain profile. / 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 / Ribonuclease H domain / RNase H type-1 domain profile. / 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: 1.6 Å
AuthorsEgli, M. / Pallan, P.S.
CitationJournal: Chem.Commun.(Camb.) / Year: 2009
Title: A conformational transition in the structure of a 2'-thiomethyl-modified DNA visualized at high resolution.
Authors: Pallan, P.S. / Prakash, T.P. / Li, F. / Eoff, R.L. / Manoharan, M. / Egli, M.
History
DepositionOct 17, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 28, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 6, 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: 5'-D(*CP*GP*CP*GP*AP*AP*(USM)P*(USM)P*CP*GP*CP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9205
Polymers19,6442
Non-polymers2763
Water1,856103
1
A: Ribonuclease H
B: 5'-D(*CP*GP*CP*GP*AP*AP*(USM)P*(USM)P*CP*GP*CP*G)-3'
hetero molecules

A: Ribonuclease H
B: 5'-D(*CP*GP*CP*GP*AP*AP*(USM)P*(USM)P*CP*GP*CP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,84010
Polymers39,2874
Non-polymers5536
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area5620 Å2
ΔGint-13 kcal/mol
Surface area17070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.930, 66.620, 38.770
Angle α, β, γ (deg.)90.00, 103.30, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Ribonuclease H / RNase H


Mass: 15916.004 Da / Num. of mol.: 1 / Fragment: RNase H domain, UNP residues 59-196 / Mutation: D132N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus halodurans (bacteria) / Gene: rnhA, BH0863 / References: UniProt: Q9KEI9, ribonuclease H
#2: DNA chain 5'-D(*CP*GP*CP*GP*AP*AP*(USM)P*(USM)P*CP*GP*CP*G)-3'


Mass: 3727.522 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Chemically synthesized modified dodecamer DNA (oligonucleotide)
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / 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: 2.62 Å3/Da / Density % sol: 53.07 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.1 M Sodium Acetate (pH 4.6), 0.2 M ammonium sulphate, 25% PEG 4000., VAPOR DIFFUSION, SITTING DROP, temperature 291K
Components of the solutions
IDNameCrystal-IDSol-ID
1Sodium Acetate11
2ammonium sulphate11
3PEG 400011
4Sodium Acetate12
5ammonium sulphate12
6PEG 400012

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9785 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 20, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. all: 26658 / Num. obs: 26499 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 363.5
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 5 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 9.9 / Num. unique all: 2562 / % possible all: 96.9

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Processing

Software
NameClassification
MAR345data collection
MOLREPphasing
SHELXL-97refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3D0P, USING THE PROTEIN MOLECULE ALONE.

3d0p


Resolution: 1.6→50 Å / Cross valid method: THROUGHOUT / σ(I): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.261 2634 -Random
Rwork0.193 ---
obs0.193 23865 100 %-
all-26449 --
Refinement stepCycle: LAST / Resolution: 1.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1114 245 18 103 1480
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.009
X-RAY DIFFRACTIONs_angle_d0.026

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