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- PDB-3svz: Crystal structure of apo BT_2972, a methyltransferase from Bacter... -

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Basic information

Entry
Database: PDB / ID: 3svz
TitleCrystal structure of apo BT_2972, a methyltransferase from Bacteroides thetaiotaomicron
ComponentsPutative methyltransferase
KeywordsTRANSFERASE / Rossmann fold / methyltransferase / S-Adenosyl methionine / S-Adenosyl-L-homocysteine / 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
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsKumar, V. / Sivaraman, J.
CitationJournal: To be published
Title: Crystal structure of apo BT_2972, a methyltransferase from Bacteroides thetaiotaomicron
Authors: Kumar, V. / Sivaraman, J.
History
DepositionJul 13, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 7, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 28, 2011Group: Refinement description
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.3Nov 1, 2023Group: Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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


Theoretical massNumber of molelcules
Total (without water)60,6362
Polymers60,6362
Non-polymers00
Water1,838102
1
A: Putative methyltransferase


Theoretical massNumber of molelcules
Total (without water)30,3181
Polymers30,3181
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putative methyltransferase


Theoretical massNumber of molelcules
Total (without water)30,3181
Polymers30,3181
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.547, 74.375, 117.110
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: 30317.943 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria)
Strain: VPI-5482 / Gene: BT_2972, NP_811884.1 / Plasmid: pGS21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q8A3I2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / 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: 2.1 Å3/Da / Density % sol: 41.38 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.12M Magnesium acetate and 16% PEG 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: Dec 4, 2010
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: 11731 / % possible obs: 95.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 0 / Redundancy: 8 % / Rsym value: 0.109 / Net I/σ(I): 10.6
Reflection shellResolution: 2.9→3 Å / Redundancy: 5.1 % / Mean I/σ(I) obs: 3.5 / Rsym value: 0.177 / % possible all: 91

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Processing

Software
NameVersionClassification
PROTEUM PLUSPLUSdata collection
MOLREPphasing
PHASERphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 3F4K

3f4k


Resolution: 2.9→50 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2692 674 5 %Random
Rwork0.2 ---
obs0.2692 9626 --
all-11083 --
Refinement stepCycle: LAST / Resolution: 2.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3962 0 0 102 4064
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.17213
X-RAY DIFFRACTIONc_bond_d0.00811
X-RAY DIFFRACTIONc_mcangle_it1.483
X-RAY DIFFRACTIONc_mcbond_it0.921

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