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- PDB-3t7s: Crystal structure of complex of SAM and BVU_3255, a methyltransfe... -

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Basic information

Entry
Database: PDB / ID: 3t7s
TitleCrystal structure of complex of SAM and BVU_3255, a methyltransferase from Bacteroides vulgatus ATCC 8482
ComponentsPutative methyltransferase
KeywordsTRANSFERASE / Small molecule methyltransferase / BVU_3255 / ROSSMANN FOLD / METHYLTRASNFERASE / SAM / Methylation
Function / homology
Function and homology information


methyltransferase activity / methylation
Similarity search - Function
: / 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
S-ADENOSYLMETHIONINE / Methyltransferase domain-containing protein
Similarity search - Component
Biological speciesBacteroides vulgatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsKumar, V. / Sivaraman, J.
CitationJournal: J.Struct.Biol. / Year: 2011
Title: Structural characterization of BVU_3255, a methyltransferase from human intestine antibiotic resistant pathogen Bacteroides vulgatus
Authors: Kumar, V. / Sivaraman, J.
History
DepositionJul 31, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 12, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Refinement description / Category: software
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative methyltransferase
B: Putative methyltransferase
C: Putative methyltransferase
D: Putative methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,2538
Polymers122,6594
Non-polymers1,5944
Water7,368409
1
A: Putative methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0632
Polymers30,6651
Non-polymers3981
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putative methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0632
Polymers30,6651
Non-polymers3981
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Putative methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0632
Polymers30,6651
Non-polymers3981
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Putative methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0632
Polymers30,6651
Non-polymers3981
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.419, 106.648, 133.004
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Putative methyltransferase


Mass: 30664.715 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: METHYLTRANSFERASE / Source: (gene. exp.) Bacteroides vulgatus (bacteria) / Strain: ATCC 8482 / Gene: BVU_3255 / Plasmid: pGS21a / Production host: Escherichia coli (E. coli) / Strain (production host): (DE3)BL21 / References: UniProt: A6L5C0
#2: Chemical
ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H22N6O5S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 409 / 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: 2.12 Å3/Da / Density % sol: 42.05 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 150mM NH4Cl, 17% w/v PEG 3350, 3% v/v 2-Propanol, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 11, 2010
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 53257 / Num. obs: 53257 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rsym value: 0.049 / Net I/σ(I): 21.05
Reflection shellResolution: 2.2→2.28 Å / Mean I/σ(I) obs: 4.5 / Rsym value: 0.374 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPMRphasing
CNS1.21refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3E7P

3e7p


Resolution: 2.2→30 Å / Occupancy max: 1 / Occupancy min: 1 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.267 2176 -RANDOM
Rwork0.23 ---
obs0.23 43686 81.3 %-
all-53728 --
Solvent computationBsol: 39.7729 Å2
Displacement parametersBiso max: 77.2 Å2 / Biso mean: 41.552 Å2 / Biso min: 15.78 Å2
Baniso -1Baniso -2Baniso -3
1-18.392 Å20 Å20 Å2
2---4.173 Å20 Å2
3----14.219 Å2
Refinement stepCycle: LAST / Resolution: 2.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7659 0 108 409 8176
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.28
X-RAY DIFFRACTIONc_mcbond_it1.3331.5
X-RAY DIFFRACTIONc_scbond_it1.9322
X-RAY DIFFRACTIONc_mcangle_it2.1392
X-RAY DIFFRACTIONc_scangle_it2.8272.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5sam.paramsam.top

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