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- PDB-6gcf: DNA binding domain of restriction endonuclease McrBC in complex w... -

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Basic information

Entry
Database: PDB / ID: 6gcf
TitleDNA binding domain of restriction endonuclease McrBC in complex with N4-methylcytosine DNA
Components
  • 5-methylcytosine-specific restriction enzyme B
  • DNA (5'-D(*GP*AP*GP*AP*CP*CP*GP*GP*TP*AP*GP*C)-3')
  • DNA (5'-D(*GP*CP*TP*AP*(C34)P*CP*GP*GP*TP*CP*TP*C)-3')
KeywordsDNA BINDING PROTEIN / N4-methylcytosine / restriction endonuclease / McrBC / base flipping
Function / homology
Function and homology information


restriction endodeoxyribonuclease activity / endonuclease complex / double-stranded methylated DNA binding / hemi-methylated DNA-binding / DNA catabolic process / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters / DNA restriction-modification system / endonuclease activity / GTPase activity / GTP binding ...restriction endodeoxyribonuclease activity / endonuclease complex / double-stranded methylated DNA binding / hemi-methylated DNA-binding / DNA catabolic process / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters / DNA restriction-modification system / endonuclease activity / GTPase activity / GTP binding / ATP hydrolysis activity / DNA binding / ATP binding / identical protein binding
Similarity search - Function
Metal Transport, Frataxin; Chain A - #90 / Type IV methyl-directed restriction enzyme EcoKMcrB subunit, DNA-binding domain / MrcB-like, N-terminal domain / : / Metal Transport, Frataxin; Chain A / 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 ...Metal Transport, Frataxin; Chain A - #90 / Type IV methyl-directed restriction enzyme EcoKMcrB subunit, DNA-binding domain / MrcB-like, N-terminal domain / : / Metal Transport, Frataxin; Chain A / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Type IV methyl-directed restriction enzyme EcoKMcrB subunit
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsSasnauskas, G.
Funding supportLithuania, 1items
OrganizationGrant numberCountry
Research Council of Lithuania, MIP-027/2012Lithuania
CitationJournal: FEBS Lett. / Year: 2018
Title: Recognition of modified cytosine variants by the DNA-binding domain of methyl-directed endonuclease McrBC.
Authors: Zagorskaite, E. / Manakova, E. / Sasnauskas, G.
History
DepositionApr 17, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 19, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 24, 2018Group: Data collection / 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_author.identifier_ORCID
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 5-methylcytosine-specific restriction enzyme B
B: 5-methylcytosine-specific restriction enzyme B
C: DNA (5'-D(*GP*AP*GP*AP*CP*CP*GP*GP*TP*AP*GP*C)-3')
D: DNA (5'-D(*GP*CP*TP*AP*(C34)P*CP*GP*GP*TP*CP*TP*C)-3')


Theoretical massNumber of molelcules
Total (without water)46,6614
Polymers46,6614
Non-polymers00
Water4,756264
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5080 Å2
ΔGint-16 kcal/mol
Surface area17330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.280, 69.675, 145.054
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 5-methylcytosine-specific restriction enzyme B / EcoKMcrBC


Mass: 19659.920 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: mcrB, rglB, b4346, JW5871
Production host: Escherichia coli str. K-12 substr. DH10B (bacteria)
References: UniProt: P15005, Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters
#2: DNA chain DNA (5'-D(*GP*AP*GP*AP*CP*CP*GP*GP*TP*AP*GP*C)-3')


Mass: 3712.430 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*GP*CP*TP*AP*(C34)P*CP*GP*GP*TP*CP*TP*C)-3')


Mass: 3628.381 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.: 264 / 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: 1.96 Å3/Da / Density % sol: 37.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.2 M LiCl, 17% PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 26, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.55→62.81 Å / Num. obs: 108317 / % possible obs: 99.88 % / Redundancy: 6.5 % / Biso Wilson estimate: 21.29 Å2 / Rmerge(I) obs: 0.04035 / Net I/σ(I): 28.36
Reflection shellResolution: 1.55→1.605 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.4023 / Mean I/σ(I) obs: 5.38 / Num. unique obs: 10618 / % possible all: 99.16

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Processing

Software
NameVersionClassification
PHENIX1.8.3_1479refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ssc

3ssc


Resolution: 1.55→62.81 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / Phase error: 17.01
RfactorNum. reflection% reflection
Rfree0.1784 10979 10.14 %
Rwork0.1344 --
obs0.1389 108317 97.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.55→62.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2425 487 0 264 3176
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0183692
X-RAY DIFFRACTIONf_angle_d1.4575144
X-RAY DIFFRACTIONf_dihedral_angle_d22.4581365
X-RAY DIFFRACTIONf_chiral_restr0.07547
X-RAY DIFFRACTIONf_plane_restr0.009493
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.58510.19733770.14153278X-RAY DIFFRACTION100
1.5851-1.60590.19953510.13033355X-RAY DIFFRACTION100
1.6059-1.62790.21963680.13673303X-RAY DIFFRACTION100
1.6279-1.65120.19193930.11833381X-RAY DIFFRACTION100
1.6512-1.67580.18543920.11423280X-RAY DIFFRACTION100
1.6758-1.7020.17933710.11553337X-RAY DIFFRACTION100
1.702-1.72990.19813170.11363408X-RAY DIFFRACTION100
1.7299-1.75980.18213700.10553267X-RAY DIFFRACTION100
1.7598-1.79180.15753900.10043298X-RAY DIFFRACTION99
1.7918-1.82620.16273690.10353397X-RAY DIFFRACTION100
1.8262-1.86350.17964010.11063271X-RAY DIFFRACTION100
1.8635-1.9040.17683980.10683319X-RAY DIFFRACTION100
1.904-1.94830.17313300.11383333X-RAY DIFFRACTION100
1.9483-1.99710.18393560.11193346X-RAY DIFFRACTION100
1.9971-2.05110.18323770.10893388X-RAY DIFFRACTION100
2.0511-2.11140.17793580.11773339X-RAY DIFFRACTION100
2.1114-2.17960.17293900.11353308X-RAY DIFFRACTION99
2.1796-2.25750.18053730.11813329X-RAY DIFFRACTION100
2.2575-2.34790.1783690.12393269X-RAY DIFFRACTION100
2.3479-2.45470.17493730.12523412X-RAY DIFFRACTION100
2.4547-2.58420.19343720.13723331X-RAY DIFFRACTION100
2.5842-2.74610.19954050.14653238X-RAY DIFFRACTION100
2.7461-2.95810.18273650.1423358X-RAY DIFFRACTION100
2.9581-3.25580.19613620.15163352X-RAY DIFFRACTION100
3.2558-3.72690.16124100.14053311X-RAY DIFFRACTION100
3.7269-4.69540.15373980.12883281X-RAY DIFFRACTION100
4.6954-62.810.183900.16863331X-RAY DIFFRACTION100

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