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- PDB-3t7r: Crystal structure of apo BVU_3255, a methyltransferase from Bacte... -

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Basic information

Entry
Database: PDB / ID: 3t7r
TitleCrystal structure of apo 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
3-[(2Z)-3-methylpent-2-en-1-yl]benzene-1,2-diol / Methyltransferase domain-containing protein
Similarity search - Component
Biological speciesBacteroides vulgatus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.9 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)61,7144
Polymers61,3292
Non-polymers3852
Water1,820101
1
A: Putative methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,8572
Polymers30,6651
Non-polymers1921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putative methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,8572
Polymers30,6651
Non-polymers1921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)132.063, 72.140, 55.893
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Putative methyltransferase


Mass: 30664.715 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
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-6PP / 3-[(2Z)-3-methylpent-2-en-1-yl]benzene-1,2-diol


Mass: 192.254 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H16O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 101 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsTHE LIGAND 6PP HAS BEEN BUILT BASED ON THE DENSITY OF THIS STRUCTURE. THE ORIGINAL COMPOUND MIGHT ...THE LIGAND 6PP HAS BEEN BUILT BASED ON THE DENSITY OF THIS STRUCTURE. THE ORIGINAL COMPOUND MIGHT BE 2-POLYPRENYLE-6-HYDROXYPHENOL, WITH 5-9 PRENYL REPEAT UNIT. ONLY A PARTIAL MODEL OF THE PROPOSED SUBSTRATE WAS BUILT, AND THE CHIRALITY OF THE ATOM CAK IS NOT THOROUGHLY VERIFIED.

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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: 2.17 Å3/Da / Density % sol: 43.33 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 170mM Mg(CH3COO)2, 15% Polyethylene Glycol 3350, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Mar 11, 2011
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 11578 / % possible obs: 92.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rsym value: 0.105 / Net I/σ(I): 23.3
Reflection shellResolution: 2.9→3 Å / Mean I/σ(I) obs: 4.8 / Rsym value: 0.184 / % possible all: 74.5

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Processing

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

3e7p


Resolution: 2.9→30 Å / Occupancy max: 1 / Occupancy min: 1 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2648 735 3.2 %Random
Rwork0.2283 ---
obs-10874 --
Solvent computationBsol: 8.2466 Å2
Displacement parametersBiso max: 67.07 Å2 / Biso mean: 40.849 Å2 / Biso min: 1 Å2
Baniso -1Baniso -2Baniso -3
1--13.062 Å20 Å20 Å2
2--4.103 Å20 Å2
3---8.96 Å2
Refinement stepCycle: LAST / Resolution: 2.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3990 0 28 101 4119
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_d1.187
X-RAY DIFFRACTIONc_mcbond_it1.0121.5
X-RAY DIFFRACTIONc_scbond_it1.3762
X-RAY DIFFRACTIONc_mcangle_it1.7492
X-RAY DIFFRACTIONc_scangle_it2.2052.5
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 DIFFRACTION5DRG.paramDRG.top

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