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

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Basic information

Entry
Database: PDB / ID: 6gcd
TitleDNA binding domain of restriction endonuclease McrBC in complex with 5-hydroxymethylcytosine DNA
Components
  • 5-methylcytosine-specific restriction enzyme B
  • DNA (5'-D(*GP*AP*GP*AP*(5HC)P*CP*GP*GP*TP*AP*GP*C)-3')
  • DNA (5'-D(*GP*CP*TP*AP*(5HC)P*CP*GP*GP*TP*CP*TP*C)-3')
KeywordsDNA BINDING PROTEIN / 5-hydroxymethylcytosine / 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 / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSasnauskas, G. / Manakova, E.
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*(5HC)P*CP*GP*GP*TP*AP*GP*C)-3')
D: DNA (5'-D(*GP*CP*TP*AP*(5HC)P*CP*GP*GP*TP*CP*TP*C)-3')


Theoretical massNumber of molelcules
Total (without water)46,8594
Polymers46,8594
Non-polymers00
Water3,927218
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4900 Å2
ΔGint-21 kcal/mol
Surface area18480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.071, 68.934, 143.708
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: 19736.037 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*(5HC)P*CP*GP*GP*TP*AP*GP*C)-3')


Mass: 3742.456 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*GP*CP*TP*AP*(5HC)P*CP*GP*GP*TP*CP*TP*C)-3')


Mass: 3644.380 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.: 218 / 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: 1.91 Å3/Da / Density % sol: 35.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 5.5
Details: 10 mM Bis-Tris, pH 5.5, 0.2 M ammonium-acetate and 14% PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU R-AXIS IV / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 1, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.8→23.88 Å / Num. obs: 64054 / % possible obs: 99.83 % / Redundancy: 18.3 % / Biso Wilson estimate: 22.8 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 48.73
Reflection shellResolution: 1.8→1.864 Å / Redundancy: 15 % / Rmerge(I) obs: 0.451 / Mean I/σ(I) obs: 0.0548 / Num. unique obs: 6694 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ssc

3ssc


Resolution: 1.8→23.879 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.27 / Phase error: 20.47
RfactorNum. reflection% reflection
Rfree0.214 6465 10.09 %
Rwork0.1658 --
obs0.1706 64054 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.8→23.879 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2565 490 0 218 3273
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0183781
X-RAY DIFFRACTIONf_angle_d1.5255326
X-RAY DIFFRACTIONf_dihedral_angle_d13.8622630
X-RAY DIFFRACTIONf_chiral_restr0.1552
X-RAY DIFFRACTIONf_plane_restr0.01518
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.82040.3122100.26741939X-RAY DIFFRACTION100
1.8204-1.84190.31572180.24941920X-RAY DIFFRACTION100
1.8419-1.86430.2961870.22241929X-RAY DIFFRACTION100
1.8643-1.88790.25452230.2031926X-RAY DIFFRACTION100
1.8879-1.91270.25762210.19631934X-RAY DIFFRACTION100
1.9127-1.93890.25092390.19171851X-RAY DIFFRACTION100
1.9389-1.96660.25482150.18231943X-RAY DIFFRACTION100
1.9666-1.99590.21862490.17541923X-RAY DIFFRACTION100
1.9959-2.02710.24732010.17431901X-RAY DIFFRACTION100
2.0271-2.06030.24782170.18641908X-RAY DIFFRACTION100
2.0603-2.09580.2412120.18251962X-RAY DIFFRACTION100
2.0958-2.13390.25052360.16391875X-RAY DIFFRACTION100
2.1339-2.17490.20122410.16681905X-RAY DIFFRACTION100
2.1749-2.21930.23172430.1641928X-RAY DIFFRACTION100
2.2193-2.26750.20962110.15471903X-RAY DIFFRACTION100
2.2675-2.32020.25172110.15741906X-RAY DIFFRACTION100
2.3202-2.37820.21552010.15661975X-RAY DIFFRACTION100
2.3782-2.44250.22591950.16411922X-RAY DIFFRACTION100
2.4425-2.51420.2852220.17961902X-RAY DIFFRACTION100
2.5142-2.59530.2282040.17621949X-RAY DIFFRACTION99
2.5953-2.68790.26621920.17631898X-RAY DIFFRACTION99
2.6879-2.79540.21632140.17521941X-RAY DIFFRACTION99
2.7954-2.92240.20392160.16931890X-RAY DIFFRACTION100
2.9224-3.07620.24421930.16531940X-RAY DIFFRACTION100
3.0762-3.26850.21012090.1671959X-RAY DIFFRACTION100
3.2685-3.52010.20392230.14981863X-RAY DIFFRACTION100
3.5201-3.8730.18922070.14961937X-RAY DIFFRACTION100
3.873-4.43030.15131930.13641955X-RAY DIFFRACTION100
4.4303-5.57010.17082230.13851913X-RAY DIFFRACTION100
5.5701-23.8810.18342390.18331892X-RAY DIFFRACTION99

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