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Basic information

Entry
Database: PDB / ID: 4zcf
TitleStructural basis of asymmetric DNA methylation and ATP-triggered long-range diffusion by EcoP15I
Components
  • (Restriction endonuclease EcoP15I, ...) x 2
  • DNA 20-mer AATCATAGTCTACTGCTGTA
  • DNA 20-mer ATACAGCAGTAGACTATGAT
KeywordsHydrolase-DNA complex / Hydrolase/DNA / ATP motor / DNA methyltransferase / Asymmetric DNA methylation
Function / homology
Function and homology information


N-methyltransferase activity / site-specific DNA-methyltransferase (adenine-specific) / site-specific DNA-methyltransferase (adenine-specific) activity / endonuclease activity / DNA binding / ATP binding
Similarity search - Function
Type III R-M EcoP15I, C-terminal / Type III R-M EcoP15I C-terminal domain / Endonuclease domain / N4/N6-methyltransferase, Type III restriction-modification enzyme EcoPI Mod subunit-like / DNA methylase N-4/N-6 / DNA methylase / N-6 Adenine-specific DNA methylases signature. / DNA methylase, N-6 adenine-specific, conserved site / Helicase/UvrB, N-terminal / Type III restriction enzyme, res subunit ...Type III R-M EcoP15I, C-terminal / Type III R-M EcoP15I C-terminal domain / Endonuclease domain / N4/N6-methyltransferase, Type III restriction-modification enzyme EcoPI Mod subunit-like / DNA methylase N-4/N-6 / DNA methylase / N-6 Adenine-specific DNA methylases signature. / DNA methylase, N-6 adenine-specific, conserved site / Helicase/UvrB, N-terminal / Type III restriction enzyme, res subunit / S-adenosyl-L-methionine-dependent methyltransferase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / : / DNA / DNA (> 10) / Site-specific DNA-methyltransferase (adenine-specific) / Restriction endonuclease EcoP15I, restriction subunit
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.6 Å
AuthorsGupta, Y.K. / Chan, S.H. / Xu, S.Y. / Aggarwal, A.K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM111507 United States
CitationJournal: Nat Commun / Year: 2015
Title: Structural basis of asymmetric DNA methylation and ATP-triggered long-range diffusion by EcoP15I.
Authors: Gupta, Y.K. / Chan, S.H. / Xu, S.Y. / Aggarwal, A.K.
History
DepositionApr 15, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Derived calculations / Source and taxonomy
Category: entity_src_gen / pdbx_audit_support ...entity_src_gen / pdbx_audit_support / pdbx_entity_src_syn / pdbx_struct_oper_list
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Jan 20, 2021Group: Derived calculations / Polymer sequence
Category: entity_poly / pdbx_struct_conn_angle / struct_conn
Item: _entity_poly.type / _pdbx_struct_conn_angle.ptnr1_auth_asym_id ..._entity_poly.type / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 2.1Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Restriction endonuclease EcoP15I, modification subunit
B: Restriction endonuclease EcoP15I, modification subunit
C: Restriction endonuclease EcoP15I, restriction subunit
D: DNA 20-mer ATACAGCAGTAGACTATGAT
E: DNA 20-mer AATCATAGTCTACTGCTGTA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)272,2629
Polymers271,7655
Non-polymers4974
Water1,71195
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22000 Å2
ΔGint-113 kcal/mol
Surface area83990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.838, 101.838, 533.031
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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Restriction endonuclease EcoP15I, ... , 2 types, 3 molecules ABC

#1: Protein Restriction endonuclease EcoP15I, modification subunit


Mass: 74190.719 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ecoP15Imod / Production host: Escherichia coli (E. coli) / Strain (production host): NEB Express / References: UniProt: Q5ZND1
#2: Protein Restriction endonuclease EcoP15I, restriction subunit


Mass: 111109.641 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ecoP15Ires / Production host: Escherichia coli (E. coli) / Strain (production host): NEB Express / References: UniProt: Q5ZND2

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DNA chain , 2 types, 2 molecules DE

#3: DNA chain DNA 20-mer ATACAGCAGTAGACTATGAT


Mass: 6166.030 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)
#4: DNA chain DNA 20-mer AATCATAGTCTACTGCTGTA


Mass: 6107.978 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)

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Non-polymers , 4 types, 99 molecules

#5: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#6: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#7: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 95 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.54 Å3/Da / Density % sol: 51.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: PEG 5000 monomethylether, potassium acetate, HEPES / PH range: 7.2-7.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 21, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 85834 / % possible obs: 97.3 % / Redundancy: 15.1 % / Biso Wilson estimate: 73.1 Å2 / Rsym value: 0.11 / Net I/σ(I): 15.5
Reflection shellHighest resolution: 2.6 Å / Redundancy: 15 % / Rmerge(I) obs: 0.72 / Mean I/σ(I) obs: 3.4 / % possible all: 94.5

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
XDSdata reduction
SCALAdata scaling
SHARPphasing
RefinementMethod to determine structure: MIR / Resolution: 2.6→40 Å / Cor.coef. Fo:Fc: 0.9142 / Cor.coef. Fo:Fc free: 0.8813 / SU R Cruickshank DPI: 0.433 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.43 / SU Rfree Blow DPI: 0.282 / SU Rfree Cruickshank DPI: 0.287
RfactorNum. reflection% reflectionSelection details
Rfree0.2625 4321 5.04 %RANDOM
Rwork0.2183 ---
obs0.2206 85658 97.45 %-
Displacement parametersBiso mean: 59.93 Å2
Baniso -1Baniso -2Baniso -3
1--4.4567 Å20 Å20 Å2
2---4.4567 Å20 Å2
3---8.9133 Å2
Refine analyzeLuzzati coordinate error obs: 0.389 Å
Refinement stepCycle: LAST / Resolution: 2.6→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13995 818 26 95 14934
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0115193HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.2520776HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d5162SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes348HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2128HARMONIC5
X-RAY DIFFRACTIONt_it15193HARMONIC20
X-RAY DIFFRACTIONt_nbd2SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.78
X-RAY DIFFRACTIONt_other_torsion20.3
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion2090SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact16288SEMIHARMONIC4
LS refinement shellResolution: 2.6→2.67 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3468 295 4.81 %
Rwork0.2712 5835 -
all0.2748 6130 -
obs--97.45 %

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