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- PDB-1eg2: CRYSTAL STRUCTURE OF RHODOBACTER SPHEROIDES (N6 ADENOSINE) METHYL... -

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Basic information

Entry
Database: PDB / ID: 1eg2
TitleCRYSTAL STRUCTURE OF RHODOBACTER SPHEROIDES (N6 ADENOSINE) METHYLTRANSFERASE (M.RSRI)
ComponentsMODIFICATION METHYLASE RSRI
KeywordsTRANSFERASE / Rossmann Fold / exocyclic amino DNA methyltransferase RsrI / DNA binding / DNA modification / DNA methylation / Structural Genomics / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
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
5'-DEOXY-5'-METHYLTHIOADENOSINE / Type II methyltransferase M.RsrI
Similarity search - Component
Biological speciesRhodobacter sphaeroides (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.75 Å
AuthorsScavetta, R.D. / Thomas, C.B. / Walsh, M.A. / Szegedi, S. / Joachimiak, A. / Gumport, R.I. / Churchill, M.E.A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: Nucleic Acids Res. / Year: 2000
Title: Structure of RsrI methyltransferase, a member of the N6-adenine beta class of DNA methyltransferases.
Authors: Scavetta, R.D. / Thomas, C.B. / Walsh, M.A. / Szegedi, S. / Joachimiak, A. / Gumport, R.I. / Churchill, M.E.
History
DepositionFeb 11, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 18, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)36,0002
Polymers35,7021
Non-polymers2971
Water4,089227
1


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

A: MODIFICATION METHYLASE RSRI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,9994
Polymers71,4042
Non-polymers5952
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area4600 Å2
ΔGint-10 kcal/mol
Surface area24110 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)70.420, 130.253, 67.284
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein MODIFICATION METHYLASE RSRI / ADENINE-SPECIFIC METHYLTRANSFERASE RSRI / M.RSRI


Mass: 35702.191 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Plasmid: PET28A
References: UniProt: P14751, site-specific DNA-methyltransferase (adenine-specific)
#2: Chemical ChemComp-MTA / 5'-DEOXY-5'-METHYLTHIOADENOSINE / 5′-Methylthioadenosine


Mass: 297.334 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H15N5O3S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 227 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.16 Å3/Da / Density % sol: 43.06 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: 1.5 M Li2SO4, 0.1 M HEPES, 0.5% NaAzide, 10 mM EDTA, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
pH: 7.4 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
11.5 M11LiSO4
2100 mMHEPES11
310 mMEDTA11

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
1931
2931
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONNSLS X12C11
SYNCHROTRONAPS 19-ID2
Detector
TypeIDDetectorDate
BRANDEIS1CCDJun 5, 1998
3x3 mosaic in house2CCDAug 14, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→35.33 Å / Num. all: 188165 / Num. obs: 68339 / % possible obs: 94.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Biso Wilson estimate: 18.9 Å2 / Rmerge(I) obs: 0.035 / Net I/σ(I): 13.2
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.242 / Num. unique all: 2281 / % possible all: 93.9
Reflection
*PLUS
Highest resolution: 1.75 Å / Lowest resolution: 20 Å / Num. obs: 20741 / Num. measured all: 69339
Reflection shell
*PLUS
% possible obs: 93.9 % / Num. unique obs: 2281 / Num. measured obs: 2873 / Mean I/σ(I) obs: 4.3

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Processing

Software
NameVersionClassification
XTAL1=MARMADdata collection
SCALEPACKdata scaling
SOLVEphasing
SHARPphasing
CNSrefinement
MARMADdata reduction
DENZOdata reduction
RefinementResolution: 1.75→35.21 Å / σ(F): 0 / σ(I): 2
Stereochemistry target values: bond violations=0.05 angle violations=8.0 dihedral violations=60.0 improper violations=3.0 reported close contacts=2.5 lower resolution limit for coordinate error estimation=5.0
RfactorNum. reflection% reflectionSelection details
Rfree0.25 3140 -random 10% pick using make_cv.inp of CNS.
Rwork0.214 ---
all-31646 --
obs-31393 99.2 %-
Refinement stepCycle: LAST / Resolution: 1.75→35.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2146 0 20 227 2393
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.0050.05
X-RAY DIFFRACTIONc_angle_deg1.38
X-RAY DIFFRACTIONc_torsion_deg22.960
X-RAY DIFFRACTIONc_torsion_impr_deg0.733
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.24 / Rfactor Rwork: 0.21
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.15
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.66
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.08
LS refinement shell
*PLUS
Highest resolution: 1.75 Å / Lowest resolution: 1.81 Å / Rfactor Rfree: 0.28 / Rfactor Rwork: 0.27

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