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- PDB-3kty: Crystal Structure of Probable Methyltransferase from Bordetella p... -

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Basic information

Entry
Database: PDB / ID: 3kty
TitleCrystal Structure of Probable Methyltransferase from Bordetella pertussis Tohama I
ComponentsProbable methyltransferase
KeywordsTRANSFERASE / alpha-beta-alpha sandwich / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG / Methyltransferase
Function / homology
Function and homology information


tRNA nucleoside ribose methylation / : / RNA binding / cytosol
Similarity search - Function
RNA methyltransferase TrmJ/LasT / tRNA/rRNA methyltransferase, SpoU type / SpoU rRNA Methylase family / SPOUT methyltransferase, trefoil knot domain / Alpha/beta knot / tRNA (guanine-N1-)-methyltransferase, N-terminal / Alpha/beta knot methyltransferases / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Probable methyltransferase
Similarity search - Component
Biological speciesBordetella pertussis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.302 Å
AuthorsKim, Y. / Tesar, C. / Keigher, L. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal Structure of Probable Methyltransferase SpoU from Bordetella pertussis Tohama I
Authors: Kim, Y. / Tesar, C. / Keigher, L. / Joachimiak, A.
History
DepositionNov 26, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 8, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable methyltransferase
B: Probable methyltransferase
C: Probable methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,3747
Polymers55,9973
Non-polymers3764
Water2,306128
1
A: Probable methyltransferase

A: Probable methyltransferase


Theoretical massNumber of molelcules
Total (without water)37,3322
Polymers37,3322
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_657-x+1,y,-z+21
Buried area2820 Å2
ΔGint-4 kcal/mol
Surface area15260 Å2
MethodPISA
2
B: Probable methyltransferase
C: Probable methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7086
Polymers37,3322
Non-polymers3764
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3220 Å2
ΔGint-30 kcal/mol
Surface area15230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.480, 69.514, 174.802
Angle α, β, γ (deg.)90.00, 95.16, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Probable methyltransferase


Mass: 18665.768 Da / Num. of mol.: 3 / Fragment: target domain 1 - 170
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bordetella pertussis (bacteria) / Strain: Tohama I / Gene: BP1901 / Plasmid: pMCSG19 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Magic / References: UniProt: Q7VXA3
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / 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: 2.3 Å3/Da / Density % sol: 46.41 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M Lithium sulfate monohydrate, 0.1 M HEPES pH7.5, 25 % w/v Polyehtlyene glycol 3,350, VAPOR DIFFUSION, SITTING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 14, 2008 / Details: mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.3→43.52 Å / Num. all: 22535 / Num. obs: 22535 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Biso Wilson estimate: 43.52 Å2 / Rsym value: 0.117 / Net I/σ(I): 8.7
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 1.7 / Num. unique all: 1130 / Rsym value: 0.623 / % possible all: 97.5

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
SHELXSphasing
MLPHAREphasing
RESOLVEmodel building
SOLVEphasing
PHENIX(phenix.refine: 1.5_2)refinement
HKL-3000data reduction
HKL-3000data scaling
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.302→43.52 Å / SU ML: 0.36 / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 27.19 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.24 1151 5.12 %random
Rwork0.187 ---
all0.19 22502 --
obs0.19 22502 99.27 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.368 Å2 / ksol: 0.316 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-10.5154 Å20 Å2-4.0082 Å2
2---1.9174 Å20 Å2
3----8.5979 Å2
Refinement stepCycle: LAST / Resolution: 2.302→43.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3823 0 22 128 3973
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0133999
X-RAY DIFFRACTIONf_angle_d1.4095462
X-RAY DIFFRACTIONf_dihedral_angle_d19.6151454
X-RAY DIFFRACTIONf_chiral_restr0.081646
X-RAY DIFFRACTIONf_plane_restr0.008723
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.3015-2.40620.33891460.25182616276297
2.4062-2.53310.2941470.225826592806100
2.5331-2.69180.29781360.207926892825100
2.6918-2.89960.26691480.207426562804100
2.8996-3.19130.27471440.198126632807100
3.1913-3.65290.21421330.178326842817100
3.6529-4.60140.2081460.15512672281899
4.6014-43.53150.20661510.16482712286399
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDMethodL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
1refined2.9393-0.73771.67833.5531-1.72973.9265-0.0296-0.22520.2053-0.0950.1310.0746-0.2515-0.3503-0.09450.0570.03350.02010.0843-0.04150.0926-10.402230.6409104.4493
23.0523-2.30271.71651.7568-1.08424.8968-0.1903-0.13230.00910.16110.23980.0442-0.5553-0.21320.00680.3317-0.0393-0.02490.16810.02010.2254
32.10870.517-1.16452.5232-1.00836.8858-0.07010.1261-0.1550.1021-0.3099-0.2415-0.33060.0330.35360.2126-0.0024-0.05220.20950.05050.2609
Refinement TLS groupSelection details: chain C

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