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- PDB-1mxi: Structure of YibK from Haemophilus influenzae (HI0766): a Methylt... -

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Basic information

Entry
Database: PDB / ID: 1mxi
TitleStructure of YibK from Haemophilus influenzae (HI0766): a Methyltransferase with a Cofactor Bound at a Site Formed by a Knot
ComponentsHypothetical tRNA/rRNA methyltransferase HI0766
KeywordsTRANSFERASE / methyltransferase / S-adenosylhomocysteine / spoU family / Structure 2 Function Project / S2F / Structural Genomics
Function / homology
Function and homology information


wobble position cytosine ribose methylation / wobble position uridine ribose methylation / tRNA (cytidine(34)-2'-O)-methyltransferase activity / tRNA (5-carboxymethylaminomethyluridine(34)-2'-O)-methyltransferase activity / tRNA (cytidine34-2'-O)-methyltransferase / RNA binding / identical protein binding / cytoplasm
Similarity search - Function
tRNA (cytidine/uridine-2'-O-)-methyltransferase / 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
IODIDE ION / S-ADENOSYL-L-HOMOCYSTEINE / tRNA (cytidine(34)-2'-O)-methyltransferase
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsLim, K. / Zhang, H. / Tempczyk, A. / Bonander, N. / Toedt, J. / Howard, A. / Eisenstein, E. / Herzberg, O. / Structure 2 Function Project (S2F)
CitationJournal: Proteins / Year: 2003
Title: Structure of the YibK methyltransferase from Haemophilus influenzae (HI0766): a Cofactor Bound at a Site Formed by a Knot
Authors: Lim, K. / Zhang, H. / Tempczyk, A. / Krajewski, W. / Bonander, N. / Toedt, J. / Howard, A. / Eisenstein, E. / Herzberg, O.
History
DepositionOct 2, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 25, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Hypothetical tRNA/rRNA methyltransferase HI0766
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9393
Polymers18,4271
Non-polymers5112
Water2,756153
1
A: Hypothetical tRNA/rRNA methyltransferase HI0766
hetero molecules

A: Hypothetical tRNA/rRNA methyltransferase HI0766
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8776
Polymers36,8552
Non-polymers1,0234
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Unit cell
Length a, b, c (Å)40.8, 40.8, 165.8
Angle α, β, γ (deg.)90, 90, 90
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Hypothetical tRNA/rRNA methyltransferase HI0766 / yibK


Mass: 18427.414 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (bacteria) / Gene: HI0766 / Plasmid: PET17B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P44868, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Chemical ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: I
#3: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / 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: 1.87 Å3/Da / Density % sol: 34.27 %
Crystal growTemperature: 298 K
Method: vapor diffusion, hanging drop, soaking of crystal with cofactor sah
pH: 4.6
Details: 20% PMME 2000, 0.1 M sodium acetate, 0.2 M ammonium acetate, 3 % ethylene glycol, pH 4.6, Vapor diffusion, hanging drop, soaking of crystal with cofactor SAH, temperature 298K
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
112 mg/mlprotein1drop
250 mMTris-HCl1droppH7.5
30.1 mMdithiothreitol1drop
40.1 mMEDTA1drop
520 %PEG2000MME1reservoir
60.1 Msodium acetate1reservoirpH4.6
70.2 Mammonium acetate1reservoir
83 %ethylene glycol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 1, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 15394 / Num. obs: 15394 / % possible obs: 93.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.04 / Net I/σ(I): 18.5
Reflection shellResolution: 1.7→1.78 Å / Rmerge(I) obs: 0.223 / % possible all: 69.2
Reflection
*PLUS
Lowest resolution: 50 Å / Num. measured all: 281315 / Rmerge(I) obs: 0.04
Reflection shell
*PLUS
Highest resolution: 1.7 Å / % possible obs: 69.2 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB 1j85

1j85


Resolution: 1.7→20 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.254 1593 random
Rwork0.196 --
obs-14742 -
Displacement parametersBiso mean: 29 Å2
Refinement stepCycle: LAST / Resolution: 1.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1299 0 27 153 1479
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.017
X-RAY DIFFRACTIONc_angle_deg1.8
LS refinement shellResolution: 1.7→1.78 Å / Rfactor Rfree: 0.273 / Rfactor Rwork: 0.215

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