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- PDB-6p0g: N-terminal domain of Thermococcus Gammatolerans McrB bound to m5C DNA -

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Basic information

Entry
Database: PDB / ID: 6p0g
TitleN-terminal domain of Thermococcus Gammatolerans McrB bound to m5C DNA
Components
  • DNA (5'-D(P*AP*CP*CP*GP*GP*T)-3')
  • DNA (5'-D(P*TP*AP*CP*CP*GP*G)-3')
  • GTPase subunit of restriction endonuclease
KeywordsDNA BINDING PROTEIN/DNA / YTH domain / restriction endonuclease / DNA Binding Protein / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


endonuclease activity / ATP hydrolysis activity / ATP binding / metal ion binding
Similarity search - Function
ATPase, dynein-related, AAA domain / AAA domain (dynein-related subfamily) / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
DNA / GTPase subunit of restriction endonuclease
Similarity search - Component
Biological speciesThermococcus gammatolerans (archaea)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 Å
AuthorsHosford, C.J. / Chappie, J.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM120242 United States
CitationJournal: J.Biol.Chem. / Year: 2020
Title: The structure of theThermococcus gammatoleransMcrB N-terminal domain reveals a new mode of substrate recognition and specificity among McrB homologs.
Authors: Hosford, C.J. / Bui, A.Q. / Chappie, J.S.
History
DepositionMay 17, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2019Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jan 29, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GTPase subunit of restriction endonuclease
B: DNA (5'-D(P*TP*AP*CP*CP*GP*G)-3')
C: DNA (5'-D(P*AP*CP*CP*GP*GP*T)-3')


Theoretical massNumber of molelcules
Total (without water)25,3563
Polymers25,3563
Non-polymers00
Water724
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2370 Å2
ΔGint-8 kcal/mol
Surface area9650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.166, 57.304, 107.507
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein GTPase subunit of restriction endonuclease


Mass: 21737.219 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus gammatolerans (strain DSM 15229 / JCM 11827 / EJ3) (archaea)
Strain: DSM 15229 / JCM 11827 / EJ3 / Gene: TGAM_0453 / Variant: DSM 15229 / JCM 11827 / EJ3 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C5A3Z3
#2: DNA chain DNA (5'-D(P*TP*AP*CP*CP*GP*G)-3')


Mass: 1809.217 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(P*AP*CP*CP*GP*GP*T)-3')


Mass: 1809.217 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 2.5 Å3/Da / Density % sol: 50.81 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES pH 7.5, 18% PEG 3350, 0.20 M Ammonium sulfate
PH range: 7.0 - 8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.27→53.754 Å / Num. obs: 17710 / % possible obs: 99.4 % / Redundancy: 4.11 % / Net I/σ(I): 18
Reflection shellResolution: 2.27→2.45 Å / Redundancy: 3.85 % / Mean I/σ(I) obs: 2.59 / Num. unique obs: 2477 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.27→53.754 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 39.3
RfactorNum. reflection% reflection
Rfree0.2893 627 5.1 %
Rwork0.2378 --
obs0.2405 12299 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.27→53.754 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1367 246 0 4 1617
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011673
X-RAY DIFFRACTIONf_angle_d1.192312
X-RAY DIFFRACTIONf_dihedral_angle_d22.326613
X-RAY DIFFRACTIONf_chiral_restr0.058253
X-RAY DIFFRACTIONf_plane_restr0.005261
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2701-2.49860.41071540.3192857X-RAY DIFFRACTION100
2.4986-2.86010.34771360.3082879X-RAY DIFFRACTION100
2.8601-3.60330.37991580.29852901X-RAY DIFFRACTION100
3.6033-53.76850.2481790.2013035X-RAY DIFFRACTION100

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