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- PDB-3f4k: Crystal structure of a probable methyltransferase from Bacteroide... -

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Basic information

Entry
Database: PDB / ID: 3f4k
TitleCrystal structure of a probable methyltransferase from Bacteroides thetaiotaomicron. Northeast Structural Genomics target BtR309.
ComponentsPutative methyltransferase
KeywordsTRANSFERASE / methyltransferase / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
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 / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsSeetharaman, J. / Lew, S. / Wang, H. / Janjua, H. / Foote, E.L. / Xiao, R. / Nair, R. / Everett, J.K. / Acton, T.B. / Rost, B. ...Seetharaman, J. / Lew, S. / Wang, H. / Janjua, H. / Foote, E.L. / Xiao, R. / Nair, R. / Everett, J.K. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal structure of a probable methyltransferase from Bacteroides thetaiotaomicron. Northeast Structural Genomics target BtR309.
Authors: Seetharaman, J. / Lew, S. / Wang, H. / Janjua, H. / Foote, E.L. / Xiao, R. / Nair, R. / Everett, J.K. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F.
History
DepositionOct 31, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 27, 2023Group: 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: Putative methyltransferase


Theoretical massNumber of molelcules
Total (without water)29,4891
Polymers29,4891
Non-polymers00
Water1,35175
1
A: Putative methyltransferase

A: Putative methyltransferase


Theoretical massNumber of molelcules
Total (without water)58,9782
Polymers58,9782
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_675x-y+1,-y+2,-z+1/31
Buried area1650 Å2
ΔGint-9 kcal/mol
Surface area21900 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.335, 60.335, 145.145
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Putative methyltransferase


Mass: 29489.070 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria)
Gene: BT_2972, OrderedLocusNames / Plasmid: PET 21 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8A3I2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / 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: 2.59 Å3/Da / Density % sol: 52.44 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 170mM Ammonium Acetate, 85mM Na Citrate pH 5.6, 15% glycerol, 25.5% PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSLS X06SA10.979
SYNCHROTRONNSLS X4A20.979
Detector
TypeIDDetectorDate
ADSC QUANTUM 2101CCDOct 2, 2008
2
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 26321 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Biso Wilson estimate: 23.6 Å2 / Rmerge(I) obs: 0.074 / Rsym value: 0.068 / Net I/σ(I): 15
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.308 / Mean I/σ(I) obs: 9.8 / Rsym value: 0.258 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHELXSphasing
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.3→42.41 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 98986.3 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.244 1218 4.9 %RANDOM
Rwork0.211 ---
obs0.211 25112 95.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 40.5887 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 36.9 Å2
Baniso -1Baniso -2Baniso -3
1-5.55 Å20 Å20 Å2
2--5.55 Å20 Å2
3----11.1 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.33 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 2.3→42.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2055 0 0 75 2130
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.74
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.306 182 4.5 %
Rwork0.253 3845 -
obs--91.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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