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- PDB-3gu3: Crystal Structure of the methyltransferase BC_2162 in complex wit... -

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Basic information

Entry
Database: PDB / ID: 3gu3
TitleCrystal Structure of the methyltransferase BC_2162 in complex with S-Adenosyl-L-Homocysteine from Bacillus cereus, Northeast Structural Genomics Consortium Target BcR20
ComponentsMethyltransferase
KeywordsTRANSFERASE / alpha-beta protein / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG / Methyltransferase
Function / homology
Function and homology information


Transferases; Transferring one-carbon groups; Methyltransferases / methyltransferase activity / methylation
Similarity search - Function
DNA polymerase; domain 1 - #350 / Methyltransferase domain / Methyltransferase domain / Vaccinia Virus protein VP39 / DNA polymerase; domain 1 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / S-ADENOSYL-L-HOMOCYSTEINE / Methyltransferase
Similarity search - Component
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsForouhar, F. / Neely, H. / Seetharaman, J. / Ciano, C. / Ma, L. / Zhao, L. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. ...Forouhar, F. / Neely, H. / Seetharaman, J. / Ciano, C. / Ma, L. / Zhao, L. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Northeast Structural Genomics Consortium Target BcR20
Authors: Forouhar, F. / Neely, H. / Seetharaman, J. / Ciano, C. / Ma, L. / Zhao, L. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F.
History
DepositionMar 28, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 7, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Aug 24, 2011Group: Structure summary
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.contact_author / _software.contact_author_email ..._software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Methyltransferase
B: Methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,7576
Polymers65,8702
Non-polymers8874
Water5,278293
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4200 Å2
ΔGint-21 kcal/mol
Surface area23620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.793, 90.793, 122.627
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32

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Components

#1: Protein Methyltransferase /


Mass: 32935.184 Da / Num. of mol.: 2 / Fragment: BC_2162
Mutation: Substitution of Met residues by Seleno-Met residues and addition of a C-tag (lehhhhhh).
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (bacteria) / Strain: ATCC 14579 / Gene: BC_2162 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+ Magic
References: UniProt: Q81E32, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Fragment: Methyltransferase / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 293 / 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: 4.43 Å3/Da / Density % sol: 72.23 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4
Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5), and 10mM S-Adenosyl-L-Methionine . Reservoir solution: 100 mM Sodium Citrate and 5.76M Potassium Acetate , VAPOR ...Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5), and 10mM S-Adenosyl-L-Methionine . Reservoir solution: 100 mM Sodium Citrate and 5.76M Potassium Acetate , VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97905 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 10, 2007 / Details: Mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97905 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. all: 100547 / Num. obs: 100246 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 20.1 Å2 / Rmerge(I) obs: 0.083 / Rsym value: 0.066 / Net I/σ(I): 14.3
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2.98 / Num. unique all: 10106 / Rsym value: 0.479 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
CNS1.2 & XtalViewrefinement
PDB_EXTRACT3data extraction
ADSCQuantumdata collection
HKL-2000data reduction
SCALEPACKdata scaling
SnB& SOLVE/RESOLVEphasing
REFMACrefinement
RefinementMethod to determine structure: SAD / Resolution: 2.3→19.92 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 314365.531 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.212 4337 4.9 %RANDOM
Rwork0.184 ---
all0.187 100461 --
obs0.185 89210 88.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 58.8 Å2 / ksol: 0.45 e/Å3
Displacement parametersBiso mean: 35.2 Å2
Baniso -1Baniso -2Baniso -3
1-0.41 Å20 Å20 Å2
2--0.41 Å20 Å2
3----0.83 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 2.3→19.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4424 0 60 293 4777
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d23
X-RAY DIFFRACTIONc_improper_angle_d0.74
LS refinement shellResolution: 2.3→2.38 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.241 319 4.4 %
Rwork0.217 6875 -
obs-7194 71.1 %

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