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- PDB-3sxj: Crystal structure of complex of BT_2972 and AdoMet, a methyltrans... -

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Basic information

Entry
Database: PDB / ID: 3sxj
TitleCrystal structure of complex of BT_2972 and AdoMet, 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


S-adenosylmethionine-dependent methyltransferase activity / 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
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsKumar, V. / Sivaraman, J.
CitationJournal: To be Published
Title: Crystal structure of complex of BT_2972 and AdoMet, a methyltransferase from Bacteroides thetaiotaomicron
Authors: Kumar, V. / Sivaraman, J.
History
DepositionJul 14, 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 ...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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,4334
Polymers60,6362
Non-polymers7972
Water1,60389
1
A: Putative methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7162
Polymers30,3181
Non-polymers3981
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putative methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7162
Polymers30,3181
Non-polymers3981
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)120.797, 59.685, 77.622
Angle α, β, γ (deg.)90.00, 104.61, 90.00
Int Tables number5
Space group name H-MC121

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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 / Plasmid: pGS21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q8A3I2
#2: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE / S-Adenosyl methionine


Mass: 398.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H22N6O5S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 2.15 Å3/Da / Density % sol: 42.92 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 25% (v/v) 2-propanol, 0.1 M MES monohydrate (pH 6.0), 18% (w/v) PEG MME 2000, 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: LN2-cooled, fixed-exit double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 18262 / Num. obs: 18262 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Rsym value: 0.058 / Net I/σ(I): 18.7
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 2.6 / Rsym value: 0.192 / % possible all: 86.9

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Processing

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

3f4k


Resolution: 2.5→50 Å / Cross valid method: Throught / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2729 1013 5 %Random
Rwork0.235 ---
obs0.235 14805 --
all-18713 --
Refinement stepCycle: LAST / Resolution: 2.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3960 0 54 89 4103
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.11831
X-RAY DIFFRACTIONc_bond_d0.007743

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