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- PDB-6ahw: Crystal structure of circular-permutated YibK methyltransferase f... -

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Basic information

Entry
Database: PDB / ID: 6ahw
TitleCrystal structure of circular-permutated YibK methyltransferase from Haemophilus influenzae
Componentscircular-permutated tRNA (cytidine(34)-2'-O)-methyltransferase
KeywordsTRANSFERASE / methyltransferase / circular permutation
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 / tRNA (guanine-N1-)-methyltransferase, N-terminal / Alpha/beta knot methyltransferases
Similarity search - Domain/homology
tRNA (cytidine(34)-2'-O)-methyltransferase
Similarity search - Component
Biological speciesHaemophilus influenzae Rd KW20 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.56 Å
AuthorsChuang, Y.C. / Lyu, P.C. / Hsu, S.T.D.
CitationJournal: J. Mol. Biol. / Year: 2019
Title: Untying a Protein Knot by Circular Permutation.
Authors: Chuang, Y.C. / Hu, I.C. / Lyu, P.C. / Hsu, S.D.
History
DepositionAug 20, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 23, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 30, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed
Revision 1.2Feb 13, 2019Group: Data collection / Database references / Category: citation / Item: _citation.title
Revision 1.3Feb 27, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Mar 27, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: circular-permutated tRNA (cytidine(34)-2'-O)-methyltransferase
B: circular-permutated tRNA (cytidine(34)-2'-O)-methyltransferase


Theoretical massNumber of molelcules
Total (without water)37,4052
Polymers37,4052
Non-polymers00
Water4,143230
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2920 Å2
ΔGint-10 kcal/mol
Surface area15670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.716, 46.941, 55.703
Angle α, β, γ (deg.)90.00, 97.45, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: _ / Auth seq-ID: 2 - 163 / Label seq-ID: 2 - 163

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein circular-permutated tRNA (cytidine(34)-2'-O)-methyltransferase / tRNA (cytidine/uridine-2'-O-)-methyltransferase TrmL


Mass: 18702.738 Da / Num. of mol.: 2 / Fragment: UNP residues 82-160,UNP residues 1-81
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae Rd KW20 (bacteria)
Strain: KW20 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P44868, tRNA (cytidine34-2'-O)-methyltransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 230 / 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: 2.28 Å3/Da / Density % sol: 46.11 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 25% PEG8000, 0.1M sodium cacodylate, 0.2M sodium acetate, pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 25, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.56→30 Å / Num. obs: 48195 / % possible obs: 99.6 % / Redundancy: 4 % / Biso Wilson estimate: 25.66 Å2 / Net I/σ(I): 23.47
Reflection shellResolution: 1.56→1.62 Å / Redundancy: 4 % / Mean I/σ(I) obs: 3.88 / Num. unique obs: 4806 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
HKL-2000data scaling
Blu-Icedata collection
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.56→29.85 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.951 / SU B: 4.348 / SU ML: 0.069 / Cross valid method: THROUGHOUT / ESU R: 0.115 / ESU R Free: 0.09 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2287 2447 5.1 %RANDOM
Rwork0.19348 ---
obs0.19526 45747 99.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 30.943 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å20 Å2-0 Å2
2---0.01 Å20 Å2
3---0.01 Å2
Refinement stepCycle: 1 / Resolution: 1.56→29.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2604 0 0 230 2834
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0192664
X-RAY DIFFRACTIONr_bond_other_d0.0020.022534
X-RAY DIFFRACTIONr_angle_refined_deg1.4891.9713590
X-RAY DIFFRACTIONr_angle_other_deg1.96535884
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4145322
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.96323.167120
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.27115490
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9551522
X-RAY DIFFRACTIONr_chiral_restr0.0890.2388
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212896
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02550
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_it3.1172.8871294
X-RAY DIFFRACTIONr_mcbond_other3.1132.8861293
X-RAY DIFFRACTIONr_mcangle_it3.1834.3221614
X-RAY DIFFRACTIONr_mcangle_other3.1824.3221615
X-RAY DIFFRACTIONr_scbond_it3.2723.2021370
X-RAY DIFFRACTIONr_scbond_other3.2713.2011371
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.3674.6471977
X-RAY DIFFRACTIONr_long_range_B_refined3.61433.6312933
X-RAY DIFFRACTIONr_long_range_B_other3.54833.2292888
X-RAY DIFFRACTIONr_rigid_bond_restr7.19835197
X-RAY DIFFRACTIONr_sphericity_free17.1715144
X-RAY DIFFRACTIONr_sphericity_bonded6.98555224
Refine LS restraints NCS

Ens-ID: 1 / Number: 9984 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.1 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.558→1.598 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 189 -
Rwork0.25 3279 -
obs--98.22 %

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