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- PDB-3sse: DNA binding domain of restriction endonuclease bound to DNA -

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Basic information

Entry
Database: PDB / ID: 3sse
TitleDNA binding domain of restriction endonuclease bound to DNA
Components
  • 5-methylcytosine-specific restriction enzyme B
  • DNA (5'-D(*A*GP*CP*TP*AP*CP*CP*GP*GP*TP*CP*TP*C)-3')
  • DNA (5'-D(*T*GP*AP*GP*AP*CP*CP*GP*GP*TP*AP*GP*C)-3')
KeywordsDNA BINDING PROTEIN/DNA / protein-DNA complex / restriction endonuclease / base flipping / DNA BINDING PROTEIN-DNA complex
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)
MethodX-RAY DIFFRACTION / molecular replacement / Resolution: 2.7 Å
AuthorsSukackaite, R. / Grazulis, S. / Siksnys, V.
CitationJournal: Nucleic Acids Res. / Year: 2012
Title: The recognition domain of the methyl-specific endonuclease McrBC flips out 5-methylcytosine.
Authors: Sukackaite, R. / Grazulis, S. / Tamulaitis, G. / Siksnys, V.
History
DepositionJul 8, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 5, 2012Group: Database references
Revision 1.2Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.3Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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(*T*GP*AP*GP*AP*CP*CP*GP*GP*TP*AP*GP*C)-3')
D: DNA (5'-D(*A*GP*CP*TP*AP*CP*CP*GP*GP*TP*CP*TP*C)-3')


Theoretical massNumber of molelcules
Total (without water)47,2644
Polymers47,2644
Non-polymers00
Water61334
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4910 Å2
ΔGint-18 kcal/mol
Surface area18000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.046, 69.087, 143.896
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 / Fragment: N-terminal DNA binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: mcrB / Plasmid: pBAD24 / Production host: Escherichia coli (E. coli) / Strain (production host): ER2267
References: UniProt: P15005, Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters
#2: DNA chain DNA (5'-D(*T*GP*AP*GP*AP*CP*CP*GP*GP*TP*AP*GP*C)-3')


Mass: 4016.623 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain DNA (5'-D(*A*GP*CP*TP*AP*CP*CP*GP*GP*TP*CP*TP*C)-3')


Mass: 3927.561 Da / Num. of mol.: 1 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / 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: 1.75 Å3/Da / Density % sol: 35.5 %
Crystal growTemperature: 292 K / Method: sitting drop / pH: 5.5
Details: 0.1 M Bis-Tris (pH 5.5), 0.2 M NH4Cl, 30% PEG4000, sitting drop, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: OTHER / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Dec 23, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→62.257 Å / Num. obs: 10488 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Rmerge(I) obs: 0.132 / Rsym value: 0.132 / Net I/σ(I): 14.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.7-2.855.70.441.7847714820.44100
2.85-3.025.70.3142.3823014390.314100
3.02-3.235.70.2373.1759113210.237100
3.23-3.495.70.1574.7708512400.157100
3.49-3.825.70.1245.9658711610.124100
3.82-4.275.60.0957.4586710460.095100
4.27-4.935.50.077952489500.077100
4.93-6.045.50.0729.444598180.072100
6.04-8.545.40.06111.534636430.061100
8.54-62.264.80.04311.118523880.04398.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
SCALA3.2.19data scaling
PDB_EXTRACT3.006data extraction
StructureStudio1.0.0data collection
MOSFLM6.2.6data reduction
MOLREP9.2.10phasing
RefinementResolution: 2.7→39.41 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.839 / SU B: 17.793 / SU ML: 0.371 / Details: U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflection
Rfree0.292 1036 9.9 %
Rwork0.216 --
obs0.223 10448 99.9 %
Solvent computationSolvent model: MASK
Displacement parametersBiso mean: 22.95 Å2
Baniso -1Baniso -2Baniso -3
1--1.36 Å20 Å20 Å2
2--2.4 Å20 Å2
3----1.04 Å2
Refinement stepCycle: LAST / Resolution: 2.7→39.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2471 486 0 34 2991
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0223632
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.8762.2815121
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2715299
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.22124.621132
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.65815411
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.421158
X-RAY DIFFRACTIONr_chiral_restr0.0580.2535
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0212493
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9221.51499
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.77922421
X-RAY DIFFRACTIONr_scbond_it2.30432133
X-RAY DIFFRACTIONr_scangle_it3.4984.52700
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.77 Å
RfactorNum. reflection% reflection
Rfree0.383 78 -
Rwork0.256 695 -
obs--100 %

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