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- PDB-1nw8: Structure of L72P mutant beta class N6-adenine DNA methyltransfer... -

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Basic information

Entry
Database: PDB / ID: 1nw8
TitleStructure of L72P mutant beta class N6-adenine DNA methyltransferase RsrI
ComponentsMODIFICATION METHYLASE RSRI
KeywordsTRANSFERASE / ADENINE DNA METHYLTRANSFERASE / ROSSMANN FOLD
Function / homology
Function and homology information


N-methyltransferase activity / site-specific DNA-methyltransferase (adenine-specific) / site-specific DNA-methyltransferase (adenine-specific) activity / DNA restriction-modification system / DNA binding
Similarity search - Function
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 / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Type II methyltransferase M.RsrI
Similarity search - Component
Biological speciesRhodobacter sphaeroides (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsThomas, C.B. / Scavetta, R.D. / Gumport, R.I. / Churchill, M.E.A.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: Structures of liganded and unliganded RsrI N6-adenine DNA methyltransferase: a distinct orientation for active cofactor binding
Authors: Thomas, C.B. / Scavetta, R.D. / Gumport, R.I. / Churchill, M.E.A.
History
DepositionFeb 5, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MODIFICATION METHYLASE RSRI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7573
Polymers35,6861
Non-polymers712
Water2,684149
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
A: MODIFICATION METHYLASE RSRI
hetero molecules

A: MODIFICATION METHYLASE RSRI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,5146
Polymers71,3722
Non-polymers1424
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area4160 Å2
ΔGint-59 kcal/mol
Surface area25050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.600, 131.380, 67.540
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Detailsthe other half of the putative dimer is related by a 2-fold rotation about the y axis

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Components

#1: Protein MODIFICATION METHYLASE RSRI


Mass: 35686.148 Da / Num. of mol.: 1 / Mutation: L72P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Gene: rsrIM / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P14751, site-specific DNA-methyltransferase (adenine-specific)
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 149 / 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: 2.22 Å3/Da / Density % sol: 44.71 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: lithium sulfate, HEPES, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
12.0 mg/mlprotein1drop
2100 mMHEPES1reservoirpH7.4
31.5 M1reservoirLi2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.0332 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Jun 8, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. all: 15461 / Num. obs: 14055 / % possible obs: 90.9 % / Biso Wilson estimate: 19 Å2 / Rsym value: 0.055
Reflection shellResolution: 2.25→2.33 Å / Num. unique all: 1296 / Rsym value: 0.119 / % possible all: 85.5
Reflection
*PLUS
Num. obs: 13692 / Rmerge(I) obs: 0.05
Reflection shell
*PLUS
% possible obs: 85.5 % / Num. unique obs: 1146 / Rmerge(I) obs: 0.199

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
CNSrefinement
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→35.8 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 766778.29 / Data cutoff high rms absF: 766778.29 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.239 1389 10.1 %RANDOM
Rwork0.195 ---
all0.195 15485 --
obs0.195 13692 88.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 32.7079 Å2 / ksol: 0.34657 e/Å3
Displacement parametersBiso mean: 28.1 Å2
Baniso -1Baniso -2Baniso -3
1--6.26 Å20 Å20 Å2
2--10.09 Å20 Å2
3----3.83 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.27 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 2.25→35.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2158 0 2 149 2309
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.78
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.171.5
X-RAY DIFFRACTIONc_mcangle_it3.222
X-RAY DIFFRACTIONc_scbond_it3.212
X-RAY DIFFRACTIONc_scangle_it4.412.5
LS refinement shellResolution: 2.25→2.39 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.285 207 9.6 %
Rwork0.217 1939 -
obs--84.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP_CBT.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2COFACTORS.PARAMCOFACTORS.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
Refinement
*PLUS
Lowest resolution: 50 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.24 / Rfactor Rwork: 0.2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.78
LS refinement shell
*PLUS
Lowest resolution: 2.33 Å / Rfactor Rfree: 0.27 / Rfactor Rwork: 0.24 / Num. reflection Rwork: 1146

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