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- PDB-7d51: Crystal structure of a truly knotted protein: cyclized YibK from ... -

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Basic information

Entry
Database: PDB / ID: 7d51
TitleCrystal structure of a truly knotted protein: cyclized YibK from Haemophilus influenzae
ComponentstRNA (cytidine(34)-2'-O)-methyltransferase
KeywordsTRANSFERASE / Topologically knotted protein / cyclized protein / SPOUT / trefoil knot
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 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.68 Å
AuthorsSriramoju, M.K. / Ko, K.T. / Hsu, S.T.D.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, Taiwan)MOST107-2628-M-001-005-MY3 Taiwan
CitationJournal: To Be Published
Title: Physico-chemical properties of a truly knotted protein without open ends
Authors: Sriramoju, M.K. / Ko, K.T. / Hsu, S.T.D.
History
DepositionSep 24, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 29, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)38,3662
Polymers38,3662
Non-polymers00
Water72140
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3430 Å2
ΔGint-12 kcal/mol
Surface area14560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.738, 68.781, 84.357
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / Refine code: _

Dom-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1GLYGLYAA1 - 1681 - 168
2LYSLYSBB1 - 1601 - 160

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Components

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


Mass: 19183.189 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd) (bacteria)
Gene: trmL, HI_0766 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P44868, tRNA (cytidine34-2'-O)-methyltransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsC-terminal residues LPETGGGGS (161-169) are sequence engineered specifically for cyclizing the ...C-terminal residues LPETGGGGS (161-169) are sequence engineered specifically for cyclizing the polypeptide chain.

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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: 2.3 Å3/Da / Density % sol: 46.44 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1M MES (pH6.5), 16% PEG 20000

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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: May 4, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.68→30 Å / Num. obs: 10224 / % possible obs: 98.2 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.041 / Rpim(I) all: 0.021 / Rrim(I) all: 0.046 / Χ2: 0.877 / Net I/σ(I): 18.4 / Num. measured all: 48699
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.68-2.784.50.5339310.890.2690.60.86590.8
2.78-2.894.70.3889910.9460.1940.4350.90997.3
2.89-3.024.90.30710060.9510.1520.3440.88599.5
3.02-3.1850.19310160.9840.0950.2150.93599.9
3.18-3.3850.11610360.9920.0580.130.88899.7
3.38-3.6450.06710160.9960.0330.0750.8999.9
3.64-44.90.04210390.9990.0210.0470.82699.2
4-4.584.80.03510260.9990.0170.0391.06599
4.58-5.764.50.02910610.9980.0150.0331.06499.2
5.76-304.30.01611020.9990.0080.0180.4297.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
HKL-2000data reduction
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MXI

1mxi


Resolution: 2.68→26.67 Å / Cor.coef. Fo:Fc: 0.905 / Cor.coef. Fo:Fc free: 0.852 / SU B: 16.463 / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.457 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3011 450 4.8 %RANDOM
Rwork0.2367 ---
obs0.2398 8872 89.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 126.9 Å2 / Biso mean: 38.775 Å2 / Biso min: 4.08 Å2
Baniso -1Baniso -2Baniso -3
1-0.41 Å20 Å20 Å2
2---0.67 Å20 Å2
3---0.26 Å2
Refinement stepCycle: final / Resolution: 2.68→26.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2518 0 0 40 2558
Biso mean---25.92 -
Num. residues----327
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0122575
X-RAY DIFFRACTIONr_angle_refined_deg1.171.6413487
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0135323
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.87121.429126
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.72515422
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7851518
X-RAY DIFFRACTIONr_chiral_restr0.0870.2341
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021966
Refine LS restraints NCS

Ens-ID: 1 / Number: 4552 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.13 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.681→2.75 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.292 12 -
Rwork0.249 393 -
obs--53.78 %

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