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- PDB-6ghc: Modification dependent EcoKMcrA restriction endonuclease -

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Basic information

Entry
Database: PDB / ID: 6ghc
TitleModification dependent EcoKMcrA restriction endonuclease
Components5-methylcytosine-specific restriction enzyme A
KeywordsHYDROLASE / HNH ENDONUCLEASE / MODIFICATION DEPENDENT RESTRICTION / 5-METHYLCYTOSINE / 5MC / 5-HYDROXYMETHYLCYTOSINE / 5HMC / BBA-ME NUCLEASE / ScoMcrA
Function / homology
Function and homology information


Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters / DNA restriction-modification system / methyl-CpG binding / endonuclease activity / zinc ion binding
Similarity search - Function
HNH endonuclease / HNH endonuclease / HNH nucleases / HNH nuclease
Similarity search - Domain/homology
Type IV methyl-directed restriction enzyme EcoKMcrA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.85 Å
AuthorsCzapinska, H. / Kowalska, M. / Zagorskaite, E. / Manakova, E. / Xu, S. / Siksnys, V. / Sasnauskas, G. / Bochtler, M.
CitationJournal: Nucleic Acids Res. / Year: 2018
Title: Activity and structure of EcoKMcrA.
Authors: Czapinska, H. / Kowalska, M. / Zagorskaite, E. / Manakova, E. / Slyvka, A. / Xu, S.Y. / Siksnys, V. / Sasnauskas, G. / Bochtler, M.
History
DepositionMay 7, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 8, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 22, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 24, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 5-methylcytosine-specific restriction enzyme A
B: 5-methylcytosine-specific restriction enzyme A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,7146
Polymers65,4522
Non-polymers2624
Water91951
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS, The SAXS data indicate that the biological dimer likely corresponds to the elongated dimer composed of two subunits A.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6830 Å2
ΔGint-110 kcal/mol
Surface area29540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.045, 90.383, 95.406
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 A / EcoKMcrA


Mass: 32726.195 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Gene: mcrA, rglA, b1159, JW1145 / Plasmid: pET15bm / Production host: Escherichia coli (E. coli)
References: UniProt: P24200, Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 51 / 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: 2.74 Å3/Da / Density % sol: 55.16 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.3 / Details: 0.1 M HEPES-CsOH, pH 7.3, 30% MPD / PH range: 7.3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 1.22021 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 11, 2012
RadiationMonochromator: KMC-1 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.22021 Å / Relative weight: 1
ReflectionResolution: 2.85→42.2 Å / Num. obs: 17013 / % possible obs: 99.1 % / Redundancy: 11.5 % / Biso Wilson estimate: 98.994 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.072 / Rsym value: 0.069 / Net I/σ(I): 20.96
Reflection shellResolution: 2.85→3.02 Å / Redundancy: 11.4 % / Mean I/σ(I) obs: 1.82 / CC1/2: 0.786 / Rrim(I) all: 1.419 / Rsym value: 1.357 / % possible all: 96.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
XDSdata reduction
XDSdata scaling
SHELXDEphasing
autoSHARPphasing
DMphasing
BUCCANEERmodel building
PARROTphasing
RefinementMethod to determine structure: SAD / Resolution: 2.85→42.19 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.928 / SU B: 22.782 / SU ML: 0.411 / Cross valid method: THROUGHOUT / ESU R Free: 0.441 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28272 1018 6 %RANDOM
Rwork0.21762 ---
obs0.22144 15993 99.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 116.679 Å2
Baniso -1Baniso -2Baniso -3
1-6.47 Å20 Å20 Å2
2--0.02 Å20 Å2
3----6.49 Å2
Refinement stepCycle: LAST / Resolution: 2.85→42.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4522 0 4 51 4577
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0194618
X-RAY DIFFRACTIONr_bond_other_d0.0020.024225
X-RAY DIFFRACTIONr_angle_refined_deg1.1311.9546243
X-RAY DIFFRACTIONr_angle_other_deg0.89139829
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9575567
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.27924.018224
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.66115818
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.7261534
X-RAY DIFFRACTIONr_chiral_restr0.0620.2674
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0215145
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02921
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_it3.9111.782274
X-RAY DIFFRACTIONr_mcbond_other3.90811.7792273
X-RAY DIFFRACTIONr_mcangle_it6.43817.6692839
X-RAY DIFFRACTIONr_mcangle_other6.43817.6712840
X-RAY DIFFRACTIONr_scbond_it3.89912.2672344
X-RAY DIFFRACTIONr_scbond_other3.89912.2682345
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.62818.2083404
X-RAY DIFFRACTIONr_long_range_B_refined10.3134942
X-RAY DIFFRACTIONr_long_range_B_other10.3084935
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.849→2.922 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.466 75 -
Rwork0.405 1085 -
obs--92.06 %

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