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

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Basic information

Entry
Database: PDB / ID: 6gce
TitleDNA binding domain of restriction endonuclease McrBC in complex with 5-formylcytosine 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*(5FC)P*CP*GP*GP*TP*CP*TP*C)-3')
KeywordsDNA BINDING PROTEIN / 5-formylcytosine / 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: 1.6 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
D: DNA (5'-D(*GP*CP*TP*AP*(5FC)P*CP*GP*GP*TP*CP*TP*C)-3')
C: DNA (5'-D(*GP*AP*GP*AP*CP*CP*GP*GP*TP*AP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)46,6754
Polymers46,6754
Non-polymers00
Water6,666370
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5110 Å2
ΔGint-19 kcal/mol
Surface area18060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.175, 69.988, 144.265
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*CP*TP*AP*(5FC)P*CP*GP*GP*TP*CP*TP*C)-3')


Mass: 3642.364 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: 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)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 370 / 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: 37.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.2 M LiCl, 22% PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1.001 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.001 Å / Relative weight: 1
ReflectionResolution: 1.6→35.09 Å / Num. obs: 92903 / % possible obs: 99.62 % / Redundancy: 6.3 % / Biso Wilson estimate: 29.46 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 17.15
Reflection shellResolution: 1.6→1.657 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.448 / Mean I/σ(I) obs: 2.39 / Num. unique obs: 9718 / % possible all: 99.92

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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: 1.6→35.089 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 0.86 / Phase error: 22.72
RfactorNum. reflection% reflection
Rfree0.2053 9430 10.15 %
Rwork0.1673 --
obs0.1712 92903 99.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.6→35.089 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2509 488 0 370 3367
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013674
X-RAY DIFFRACTIONf_angle_d1.0465187
X-RAY DIFFRACTIONf_dihedral_angle_d19.9141373
X-RAY DIFFRACTIONf_chiral_restr0.064550
X-RAY DIFFRACTIONf_plane_restr0.005498
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.61820.33713190.29982760X-RAY DIFFRACTION99
1.6182-1.63720.32232790.27812841X-RAY DIFFRACTION100
1.6372-1.65720.32093500.26842777X-RAY DIFFRACTION100
1.6572-1.67820.32673390.27122770X-RAY DIFFRACTION100
1.6782-1.70030.29762920.24942801X-RAY DIFFRACTION100
1.7003-1.72360.29462700.22772848X-RAY DIFFRACTION100
1.7236-1.74820.28113210.21952775X-RAY DIFFRACTION100
1.7482-1.77430.2533270.21882742X-RAY DIFFRACTION100
1.7743-1.8020.28213250.21392844X-RAY DIFFRACTION100
1.802-1.83150.24842760.20752823X-RAY DIFFRACTION100
1.8315-1.86310.2633520.19732729X-RAY DIFFRACTION100
1.8631-1.8970.24623410.17742817X-RAY DIFFRACTION100
1.897-1.93350.23092990.18382801X-RAY DIFFRACTION100
1.9335-1.97290.22042700.16862802X-RAY DIFFRACTION100
1.9729-2.01580.23473140.16012849X-RAY DIFFRACTION100
2.0158-2.06270.23013070.16632773X-RAY DIFFRACTION100
2.0627-2.11430.23843120.1682815X-RAY DIFFRACTION100
2.1143-2.17150.22533080.16442782X-RAY DIFFRACTION100
2.1715-2.23540.21083150.15612791X-RAY DIFFRACTION100
2.2354-2.30750.1933100.15232803X-RAY DIFFRACTION100
2.3075-2.38990.19513120.15172838X-RAY DIFFRACTION100
2.3899-2.48560.21043350.15622762X-RAY DIFFRACTION100
2.4856-2.59870.18753060.15382793X-RAY DIFFRACTION100
2.5987-2.73570.20443490.17032751X-RAY DIFFRACTION100
2.7357-2.9070.19923080.16552761X-RAY DIFFRACTION99
2.907-3.13130.21962990.16462789X-RAY DIFFRACTION99
3.1313-3.44620.17523130.15432743X-RAY DIFFRACTION98
3.4462-3.94430.16643410.14292727X-RAY DIFFRACTION98
3.9443-4.96710.15293210.12792719X-RAY DIFFRACTION98
4.9671-35.0970.17283200.17212647X-RAY DIFFRACTION96

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