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- PDB-3hnr: Crystal Structure of a probable methyltransferase BT9727_4108 fro... -

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Entry
Database: PDB / ID: 3hnr
TitleCrystal Structure of a probable methyltransferase BT9727_4108 from Bacillus thuringiensis subsp. Northeast Structural Genomics Consortium target id BuR219
Componentsprobable methyltransferase BT9727_4108
KeywordsTRANSFERASE / methyltransferase BT9727_4108 / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG / Methyltransferase / S-adenosyl-L-methionine
Function / homology
Function and homology information


S-adenosylmethionine-dependent methyltransferase activity / Transferases; Transferring one-carbon groups; Methyltransferases / methylation
Similarity search - Function
Uncharacterised methyltransferase, YrrT / Methyltransferase domain 25 / Methyltransferase domain / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Uncharacterized methyltransferase BT9727_4108
Similarity search - Component
Biological speciesBacillus thuringiensis serovar konkukian (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å
AuthorsSeetharaman, J. / Neely, H. / Sahdev, S. / Janjua, H. / Xiao, R. / Ciccosanti, C. / Foote, E.L. / Acton, T.B. / Rost, B. / Montelione, G.T. ...Seetharaman, J. / Neely, H. / Sahdev, S. / Janjua, H. / Xiao, R. / Ciccosanti, C. / Foote, E.L. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal Structure of a probable methyltransferase BT9727_4108 from Bacillus thuringiensis subsp. Northeast Structural Genomics Consortium target id BuR219
Authors: Seetharaman, J. / Neely, H. / Sahdev, S. / Janjua, H. / Xiao, R. / Ciccosanti, C. / Foote, E.L. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionMay 31, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 23, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 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: probable methyltransferase BT9727_4108


Theoretical massNumber of molelcules
Total (without water)25,3611
Polymers25,3611
Non-polymers00
Water72140
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.478, 40.478, 264.216
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322

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Components

#1: Protein probable methyltransferase BT9727_4108


Mass: 25361.328 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus thuringiensis serovar konkukian (bacteria)
Gene: BT9727_4108 / Plasmid: PET21 / Production host: Escherichia coli (E. coli)
References: UniProt: Q6HDF0, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / 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: 2.13 Å3/Da / Density % sol: 42.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 2M NH4SO4, 0.1M Bis Tris ph 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 20K, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 20, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. all: 10304 / Num. obs: 10304 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 34.1 Å2 / Rmerge(I) obs: 0.05 / Rsym value: 0.051 / Net I/σ(I): 48
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.05 / Num. unique all: 1051 / Rsym value: 0.05 / % possible all: 99

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SOLVEphasing
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.8→40.48 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 234772.95 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.256 1038 10.1 %RANDOM
Rwork0.243 ---
obs0.243 10229 98.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 28.7364 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 31.1 Å2
Baniso -1Baniso -2Baniso -3
1-5.17 Å20 Å20 Å2
2--5.17 Å20 Å2
3----10.35 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.48 Å0.32 Å
Refinement stepCycle: LAST / Resolution: 2.8→40.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1563 0 0 40 1603
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.2
X-RAY DIFFRACTIONc_improper_angle_d0.73
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.313 149 8.8 %
Rwork0.278 1549 -
obs--97.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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