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- PDB-5ffj: Structure of a nuclease-deletion mutant of the Type ISP restricti... -

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Basic information

Entry
Database: PDB / ID: 5ffj
TitleStructure of a nuclease-deletion mutant of the Type ISP restriction-modification enzyme LlaGI in complex with a DNA substrate mimic
Components
  • DNA (5'-D(P*TP*AP*GP*CP*TP*AP*AP*TP*AP*GP*AP*CP*TP*GP*GP*AP*TP*GP*GP*AP*GP*G)-3')
  • DNA (5'-D(P*TP*CP*CP*TP*CP*CP*AP*TP*CP*CP*AP*GP*TP*CP*TP*AP*TP*TP*AP*GP*CP*T)-3')
  • Endonuclease and methylase LlaGI
KeywordsDNA BINDING PROTEIN/DNA / Helicase-like ATPase / methyltransferase / DNA-binding protein / restriction-modification enzyme / DNA BINDING PROTEIN-DNA complex
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
Mrr-like domain / Restriction endonuclease / Type ISP restriction-modification enzyme LLaBIII, C-terminal specificity domain / Type ISP C-terminal specificity domain / N-6 DNA Methylase / DNA methylase, adenine-specific / 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 ...Mrr-like domain / Restriction endonuclease / Type ISP restriction-modification enzyme LLaBIII, C-terminal specificity domain / Type ISP C-terminal specificity domain / N-6 DNA Methylase / DNA methylase, adenine-specific / 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 / Restriction endonuclease type II-like / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / S-adenosyl-L-methionine-dependent methyltransferase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
DNA / DNA (> 10) / Site-specific DNA-methyltransferase (adenine-specific)
Similarity search - Component
Biological speciesLactococcus lactis (lactic acid bacteria)
unidentified (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.84 Å
AuthorsSaikrishnan, K. / Kulkarni, M. / Nirwan, N.
Funding support India, 1items
OrganizationGrant numberCountry
Wellcome DBT India Alliance500048-Z-09-Z India
CitationJournal: Nucleic Acids Res. / Year: 2016
Title: Structural insights into DNA sequence recognition by Type ISP restriction-modification enzymes
Authors: Kulkarni, M. / Nirwan, N. / van Aelst, K. / Szczelkun, M.D. / Saikrishnan, K.
History
DepositionDec 18, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 30, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 1, 2016Group: Database references
Revision 1.2Sep 27, 2017Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_detector ...citation / diffrn_detector / diffrn_source / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_detector.detector ..._citation.journal_id_CSD / _diffrn_detector.detector / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Mar 20, 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

Downloads & links

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Assembly

Deposited unit
A: Endonuclease and methylase LlaGI
D: DNA (5'-D(P*TP*CP*CP*TP*CP*CP*AP*TP*CP*CP*AP*GP*TP*CP*TP*AP*TP*TP*AP*GP*CP*T)-3')
C: DNA (5'-D(P*TP*AP*GP*CP*TP*AP*AP*TP*AP*GP*AP*CP*TP*GP*GP*AP*TP*GP*GP*AP*GP*G)-3')
B: Endonuclease and methylase LlaGI
E: DNA (5'-D(P*TP*CP*CP*TP*CP*CP*AP*TP*CP*CP*AP*GP*TP*CP*TP*AP*TP*TP*AP*GP*CP*T)-3')
F: DNA (5'-D(P*TP*AP*GP*CP*TP*AP*AP*TP*AP*GP*AP*CP*TP*GP*GP*AP*TP*GP*GP*AP*GP*G)-3')


Theoretical massNumber of molelcules
Total (without water)349,6626
Polymers349,6626
Non-polymers00
Water1448
1
A: Endonuclease and methylase LlaGI
D: DNA (5'-D(P*TP*CP*CP*TP*CP*CP*AP*TP*CP*CP*AP*GP*TP*CP*TP*AP*TP*TP*AP*GP*CP*T)-3')
C: DNA (5'-D(P*TP*AP*GP*CP*TP*AP*AP*TP*AP*GP*AP*CP*TP*GP*GP*AP*TP*GP*GP*AP*GP*G)-3')


Theoretical massNumber of molelcules
Total (without water)174,8313
Polymers174,8313
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7210 Å2
ΔGint-24 kcal/mol
Surface area50060 Å2
MethodPISA
2
B: Endonuclease and methylase LlaGI
E: DNA (5'-D(P*TP*CP*CP*TP*CP*CP*AP*TP*CP*CP*AP*GP*TP*CP*TP*AP*TP*TP*AP*GP*CP*T)-3')
F: DNA (5'-D(P*TP*AP*GP*CP*TP*AP*AP*TP*AP*GP*AP*CP*TP*GP*GP*AP*TP*GP*GP*AP*GP*G)-3')


Theoretical massNumber of molelcules
Total (without water)174,8313
Polymers174,8313
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7270 Å2
ΔGint-22 kcal/mol
Surface area58120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.400, 222.290, 117.410
Angle α, β, γ (deg.)90.00, 105.14, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Endonuclease and methylase LlaGI


Mass: 160719.688 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 166-1570
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactococcus lactis (lactic acid bacteria)
Production host: Escherichia coli (E. coli) / References: UniProt: Q93R01
#2: DNA chain DNA (5'-D(P*TP*CP*CP*TP*CP*CP*AP*TP*CP*CP*AP*GP*TP*CP*TP*AP*TP*TP*AP*GP*CP*T)-3')


Mass: 6926.485 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) unidentified (others)
#3: DNA chain DNA (5'-D(P*TP*AP*GP*CP*TP*AP*AP*TP*AP*GP*AP*CP*TP*GP*GP*AP*TP*GP*GP*AP*GP*G)-3')


Mass: 7184.658 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) unidentified (others)
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 3.15 Å3/Da / Density % sol: 60.93 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 100 mM Tris-HCl, 20%(w/v) PEG 20000, 4%(w/v) PEG 550 MME, 150 to 250 mM sodium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9797 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 20, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 2.84→50 Å / Num. obs: 101571 / % possible obs: 99.8 % / Redundancy: 2 % / Net I/σ(I): 9.6
Reflection shellResolution: 2.84→2.99 Å / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 2 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
Aimlessdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.84→50 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2621 5107 5.03 %
Rwork0.2293 --
obs0.231 101504 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.84→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17407 1813 0 8 19228
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00419756
X-RAY DIFFRACTIONf_angle_d0.76727199
X-RAY DIFFRACTIONf_dihedral_angle_d17.7977142
X-RAY DIFFRACTIONf_chiral_restr0.0323098
X-RAY DIFFRACTIONf_plane_restr0.0033233
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.84-2.87230.34421570.31053205X-RAY DIFFRACTION99
2.8723-2.90610.3391650.29963217X-RAY DIFFRACTION100
2.9061-2.94150.31031750.28853206X-RAY DIFFRACTION100
2.9415-2.97870.32831660.29013178X-RAY DIFFRACTION100
2.9787-3.01790.32441530.27643283X-RAY DIFFRACTION100
3.0179-3.05930.33521860.28293130X-RAY DIFFRACTION100
3.0593-3.1030.30941700.28713268X-RAY DIFFRACTION100
3.103-3.14930.34111660.28733169X-RAY DIFFRACTION100
3.1493-3.19850.3021730.26133189X-RAY DIFFRACTION100
3.1985-3.25090.31411720.25253236X-RAY DIFFRACTION100
3.2509-3.3070.28511710.24213180X-RAY DIFFRACTION100
3.307-3.36710.27761810.23873255X-RAY DIFFRACTION100
3.3671-3.43190.26891700.24143165X-RAY DIFFRACTION100
3.4319-3.50190.26981710.25183233X-RAY DIFFRACTION100
3.5019-3.57810.32541610.24893198X-RAY DIFFRACTION100
3.5781-3.66130.28351680.24963240X-RAY DIFFRACTION100
3.6613-3.75280.28091690.23193190X-RAY DIFFRACTION100
3.7528-3.85430.24441600.22073225X-RAY DIFFRACTION100
3.8543-3.96770.23311610.21243249X-RAY DIFFRACTION100
3.9677-4.09570.26571740.20473194X-RAY DIFFRACTION100
4.0957-4.24210.23451530.19193223X-RAY DIFFRACTION100
4.2421-4.41190.21871990.20143205X-RAY DIFFRACTION100
4.4119-4.61270.23931930.19333201X-RAY DIFFRACTION100
4.6127-4.85580.22331920.19673212X-RAY DIFFRACTION100
4.8558-5.15990.25431760.20793199X-RAY DIFFRACTION100
5.1599-5.55810.25891640.22193247X-RAY DIFFRACTION100
5.5581-6.1170.21711490.23333234X-RAY DIFFRACTION100
6.117-7.00120.29461710.22733225X-RAY DIFFRACTION100
7.0012-8.81710.25071780.21383235X-RAY DIFFRACTION100
8.8171-63.94720.22911630.23493206X-RAY DIFFRACTION98

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