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- PDB-4kdz: Crystal structure of tRNA/rRNA methyltransferase YibK from Escher... -

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Basic information

Entry
Database: PDB / ID: 4kdz
TitleCrystal structure of tRNA/rRNA methyltransferase YibK from Escherichia coli (Target NYSGRC-012599)
ComponentstRNA (cytidine(34)-2'-O)-methyltransferase
KeywordsTRANSFERASE / Structural Genomics / PSI-Biology / New York Structural Genomics Research Consortium / NYSGRC / SpoU methyltransferase / S-adenosyl-l-methionine
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 / 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 speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.32 Å
AuthorsKim, J. / Toro, R. / Bhosle, R. / Almo, S.C. / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: To be Published
Title: Crystal structure of tRNA/rRNA methyltransferase YibK from Escherichia coli (Target NYSGRC-012599)
Authors: Kim, J. / Toro, R. / Bhosle, R. / Almo, S.C.
History
DepositionApr 25, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: tRNA (cytidine(34)-2'-O)-methyltransferase


Theoretical massNumber of molelcules
Total (without water)17,7471
Polymers17,7471
Non-polymers00
Water1,04558
1
A: tRNA (cytidine(34)-2'-O)-methyltransferase

A: tRNA (cytidine(34)-2'-O)-methyltransferase


Theoretical massNumber of molelcules
Total (without water)35,4942
Polymers35,4942
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area2960 Å2
ΔGint-7 kcal/mol
Surface area13580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.435, 84.435, 78.654
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 tRNA (cytidine(34)-2'-O)-methyltransferase / tRNA (cytidine/uridine-2'-O-)-methyltransferase TrmL


Mass: 17747.225 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: UTI89 / Gene: b3606, JW3581, trmL, UTI89_C4147, yibK / Plasmid: LIC pET46a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q1R4Y9, tRNA (cytidine34-2'-O)-methyltransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / 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: 4.56 Å3/Da / Density % sol: 73.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M HEPES (pH7.5) 1.4M sodium citrate tribasic dihydrate, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 10, 2011
RadiationMonochromator: Double silicon(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.32→50 Å / Num. all: 14445 / Num. obs: 14428 / % possible obs: 99.9 % / Redundancy: 9 % / Rmerge(I) obs: 0.113 / Net I/σ(I): 17.8
Reflection shellResolution: 2.32→2.36 Å / Redundancy: 9.2 % / Rmerge(I) obs: 0.93 / Mean I/σ(I) obs: 2.7 / % possible all: 100

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Processing

Software
NameVersionClassification
CBASSdata collection
MOLREPphasing
REFMAC5.7.0029refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3N4J

3n4j


Resolution: 2.32→42.25 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.928 / SU B: 4.993 / SU ML: 0.12 / Cross valid method: THROUGHOUT / ESU R: 0.181 / ESU R Free: 0.171 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2265 689 5 %RANDOM
Rwork0.18549 ---
obs0.18763 13083 95.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.503 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20.08 Å2-0 Å2
2--0.08 Å2-0 Å2
3----0.26 Å2
Refinement stepCycle: LAST / Resolution: 2.32→42.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1228 0 0 58 1286
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0191281
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5361.9581749
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5145159
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.91622.90362
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.42715197
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.7921512
X-RAY DIFFRACTIONr_chiral_restr0.1110.2189
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0211012
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.319→2.379 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 25 -
Rwork0.215 514 -
obs--51.33 %

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