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- PDB-3ilk: The structure of a probable methylase family protein from Haemoph... -

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Basic information

Entry
Database: PDB / ID: 3ilk
TitleThe structure of a probable methylase family protein from Haemophilus influenzae Rd KW20
ComponentsUncharacterized tRNA/rRNA methyltransferase HI0380
Keywordsstructural genomics / unknown function / APC63004 / methylase family protein / Haemophilus influenzae Rd KW20 / PSI-2 / protein structure initiative / midwest center for structural genomics / MCSG / Methyltransferase / Transferase
Function / homology
Function and homology information


: / tRNA nucleoside ribose methylation / tRNA (uracil-2'-O-)-methyltransferase activity / Transferases; Transferring one-carbon groups; Methyltransferases / RNA binding / cytosol
Similarity search - Function
Helicase, Ruva Protein; domain 3 - #590 / 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 / Helicase, Ruva Protein; domain 3 / Orthogonal Bundle ...Helicase, Ruva Protein; domain 3 - #590 / 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 / Helicase, Ruva Protein; domain 3 / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Uncharacterized tRNA/rRNA methyltransferase HI_0380
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.01 Å
AuthorsTan, K. / Li, H. / Buck, K. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The structure of a probable methylase family protein from Haemophilus influenzae Rd KW20
Authors: Tan, K. / Li, H. / Buck, K. / Joachimiak, A.
History
DepositionAug 7, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 1, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized tRNA/rRNA methyltransferase HI0380
B: Uncharacterized tRNA/rRNA methyltransferase HI0380
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,31310
Polymers55,7522
Non-polymers5628
Water2,144119
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7060 Å2
ΔGint-51 kcal/mol
Surface area23140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.167, 94.392, 124.111
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsAuthors state that the biological unit is experimentally unknown. The chains A and B likely form a dimer.

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Components

#1: Protein Uncharacterized tRNA/rRNA methyltransferase HI0380


Mass: 27875.916 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (bacteria) / Strain: Rd KW20 / Gene: Haemophilus influenzae, HI0380 / Plasmid: pMCSG19 / Production host: Escherichia coli (E. coli) / Strain (production host): pPK1037
References: UniProt: P44676, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 119 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsPRO73SER IS A CLONING MUTATION COMPARED TO THE TARGET DB SEQUENCE NYSGXRC-6012A

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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: 2.53 Å3/Da / Density % sol: 51.39 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M HEPES, 10%w/v PEG8000, 8%v/v Ethylene glycol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97931 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 20, 2009 / Details: Mirror
RadiationMonochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 2→41 Å / Num. all: 36940 / Num. obs: 36940 / % possible obs: 96.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 25.9
Reflection shellResolution: 2→2.03 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.841 / Mean I/σ(I) obs: 1.4 / Num. unique all: 1411 / % possible all: 76

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
SHELXDphasing
MLPHAREphasing
DMmodel building
ARPmodel building
WARPmodel building
HKL-3000phasing
REFMAC5.5.0054refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RefinementMethod to determine structure: SAD / Resolution: 2.01→40.56 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.938 / SU B: 11.223 / SU ML: 0.138 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.191 / ESU R Free: 0.17 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24596 1838 5 %RANDOM
Rwork0.2052 ---
all0.20728 35020 --
obs0.20728 35020 96.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.914 Å2
Baniso -1Baniso -2Baniso -3
1--1.26 Å20 Å20 Å2
2--0.15 Å20 Å2
3---1.12 Å2
Refinement stepCycle: LAST / Resolution: 2.01→40.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3696 0 34 119 3849
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0223831
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5911.9775165
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0915484
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.47624.091176
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.35815717
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7141531
X-RAY DIFFRACTIONr_chiral_restr0.1140.2598
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022817
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8911.52370
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.51723806
X-RAY DIFFRACTIONr_scbond_it2.62131461
X-RAY DIFFRACTIONr_scangle_it3.8834.51351
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.013→2.065 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.337 95 -
Rwork0.273 1888 -
obs-1983 71.95 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
12.4078-0.2673-0.61032.92790.34581.260.0672-0.00090.14660.1141-0.0462-0.1377-0.0562-0.0317-0.0210.20.0087-0.02840.11-0.00080.018342.8733.94266.932
26.23181.43571.68758.0469-5.17910.1945-0.0808-0.14950.10910.2410.71450.2636-0.3618-1.6097-0.63370.29940.0491-0.01410.53610.0960.056137.24978.68196.953
32.50320.32140.75364.67740.23481.9941-0.01450.15190.0467-0.3588-0.02510.2847-0.1225-0.08520.03970.28550.0161-0.04070.09980.00740.020135.67956.31259.013
48.577-1.9455-1.398213.8008-3.00787.3364-0.02380.78130.034-1.64450.69810.72690.6102-1.5612-0.67430.659-0.1141-0.17230.83910.20550.096933.93178.10583.731
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 169
2X-RAY DIFFRACTION2A171 - 238
3X-RAY DIFFRACTION3B1 - 164
4X-RAY DIFFRACTION4B170 - 238

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