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- PDB-1j85: Structure of YibK from Haemophilus influenzae (HI0766), a truncat... -

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Basic information

Entry
Database: PDB / ID: 1j85
TitleStructure of YibK from Haemophilus influenzae (HI0766), a truncated sequence homolog of tRNA (guanosine-2'-O-) methyltransferase (SpoU)
ComponentsYibK
KeywordsTRANSFERASE / methyltransferase / structural genomics / hypothetical protein / Structure 2 Function Project / S2F
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
tRNA (cytidine(34)-2'-O)-methyltransferase
Similarity search - Component
Biological speciesHaemophilus influenzae Rd (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2 Å
AuthorsLim, K. / Zhang, H. / Toedt, J. / Tempcyzk, A. / Krajewski, W. / 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. / Tempcyzk, A. / Krajewski, W. / Bonander, N. / Toedt, J. / Howard, A. / Eisenstein, E. / Herzberg, O.
History
DepositionMay 20, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 25, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Feb 7, 2024Group: 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: YibK


Theoretical massNumber of molelcules
Total (without water)18,4271
Polymers18,4271
Non-polymers00
Water2,234124
1
A: YibK

A: YibK


Theoretical massNumber of molelcules
Total (without water)36,8552
Polymers36,8552
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area3190 Å2
ΔGint-10 kcal/mol
Surface area14380 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)40.37, 40.37, 165.82
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein YibK / HYPOTHETICAL TRNA/RRNA METHYLTRANSFERASE HI0766


Mass: 18427.414 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae Rd (bacteria) / Species: Haemophilus influenzae / Strain: KW20 / Gene: HI0766 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / 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: 1.83 Å3/Da / Density % sol: 32.87 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: protein solution (12.5 mg/ml) in 50mM Tris-HCl pH7.5, 0.1mM EDTA, 0.1mM DTT; crystallization condition - 20 % polyethylene glycol monomethylether 2000, 0.1 M Na Acetate, 0.2 M Ammonium ...Details: protein solution (12.5 mg/ml) in 50mM Tris-HCl pH7.5, 0.1mM EDTA, 0.1mM DTT; crystallization condition - 20 % polyethylene glycol monomethylether 2000, 0.1 M Na Acetate, 0.2 M Ammonium acetate, 3 % ethylene glycol, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
pH: 7.5
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: Jan 27, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 9754 / Num. obs: 9754 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.9 % / Biso Wilson estimate: 21 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 14
Reflection shellResolution: 2→2.09 Å / Redundancy: 8.7 % / Rmerge(I) obs: 0.134 / Num. unique all: 1190 / Rsym value: 0.134 / % possible all: 99.8
Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 50 Å / Num. measured all: 113016
Reflection shell
*PLUS
Highest resolution: 2 Å / % possible obs: 99.8 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
MLPHAREphasing
DMmodel building
CNSrefinement
DMphasing
RefinementMethod to determine structure: MIR / Resolution: 2→20 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.263 1036 11.1 %random
Rwork0.195 ---
all-9558 --
obs-9326 --
Displacement parametersBiso mean: 30 Å2
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1260 0 0 124 1384
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.018
X-RAY DIFFRACTIONc_angle_deg1.9
LS refinement shellResolution: 2→2.07 Å /
Rfactor% reflection
Rfree0.323 -
Rwork0.234 -
obs-94.6 %

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