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- PDB-5zyo: Crystal Structure of domain-swapped Circular-Permuted YbeA (CP74)... -

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Basic information

Entry
Database: PDB / ID: 5zyo
TitleCrystal Structure of domain-swapped Circular-Permuted YbeA (CP74) from Escherichia coli
ComponentsRibosomal RNA large subunit methyltransferase H
KeywordsTRANSFERASE / methyltransferase / domain-swapping / knot / circular permutation.
Function / homology
Function and homology information


23S rRNA (pseudouridine1915-N3)-methyltransferase / rRNA (pseudouridine-N3-)-methyltransferase activity / rRNA base methylation / rRNA methylation / ribosome binding / protein homodimerization activity / cytoplasm
Similarity search - Function
RNA methyltransferase RlmH / Predicted SPOUT methyltransferase / tRNA (guanine-N1-)-methyltransferase, N-terminal / Alpha/beta knot methyltransferases
Similarity search - Domain/homology
Ribosomal RNA large subunit methyltransferase H
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.75 Å
AuthorsKo, K.T. / Huang, K.F. / Lyu, P.C. / Hsu, S.T.D.
Funding support Taiwan, 4items
OrganizationGrant numberCountry
Ministry of Science and Technology (Taiwan)106-2113-M-001-004 Taiwan
Ministry of Science and Technology (Taiwan)107-2628-M-001-005-MY3 Taiwan
Ministry of Science and Technology (Taiwan)106-2311-B-007-004-MY3 Taiwan
Academia Sinica (Taiwan) Taiwan
CitationJournal: Structure / Year: 2019
Title: Untying a Knotted SPOUT RNA Methyltransferase by Circular Permutation Results in a Domain-Swapped Dimer.
Authors: Ko, K.T. / Hu, I.C. / Huang, K.F. / Lyu, P.C. / Hsu, S.D.
History
DepositionMay 26, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 29, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Aug 21, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Mar 27, 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

Downloads & links

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Assembly

Deposited unit
A: Ribosomal RNA large subunit methyltransferase H
B: Ribosomal RNA large subunit methyltransferase H
C: Ribosomal RNA large subunit methyltransferase H
D: Ribosomal RNA large subunit methyltransferase H


Theoretical massNumber of molelcules
Total (without water)70,5624
Polymers70,5624
Non-polymers00
Water6,323351
1
A: Ribosomal RNA large subunit methyltransferase H
C: Ribosomal RNA large subunit methyltransferase H


Theoretical massNumber of molelcules
Total (without water)35,2812
Polymers35,2812
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9390 Å2
ΔGint-67 kcal/mol
Surface area16280 Å2
MethodPISA
2
B: Ribosomal RNA large subunit methyltransferase H
D: Ribosomal RNA large subunit methyltransferase H


Theoretical massNumber of molelcules
Total (without water)35,2812
Polymers35,2812
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9080 Å2
ΔGint-69 kcal/mol
Surface area15610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.458, 88.053, 81.184
Angle α, β, γ (deg.)90.00, 101.47, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Ribosomal RNA large subunit methyltransferase H / / 23S rRNA (pseudouridine1915-N3)-methyltransferase / 23S rRNA m3Psi1915 methyltransferase / rRNA ...23S rRNA (pseudouridine1915-N3)-methyltransferase / 23S rRNA m3Psi1915 methyltransferase / rRNA (pseudouridine-N3-)-methyltransferase RlmH


Mass: 17640.424 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: rlmH, ybeA, b0636, JW0631 / Production host: Escherichia coli (E. coli)
References: UniProt: P0A8I8, 23S rRNA (pseudouridine1915-N3)-methyltransferase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 351 / 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: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.3647.79
22.3647.79
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
293.151vapor diffusion, sitting drop725% PEG 8000, 0.1M PIPES
293.152vapor diffusion, sitting drop725% PEG 8000, 0.1M PIPES

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Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
11001N
21002N
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSRRC BL15A111.00928
SYNCHROTRONNSRRC BL13B121
Detector
TypeIDDetectorDate
RAYONIX MX300HE1CCDMar 12, 2018
ADSC QUANTUM 315r2CCDDec 28, 2017
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
11.009281
211
Reflection

Entry-ID: 5ZYO / % possible obs: 99.5 %

Resolution (Å)Num. obsRedundancy (%)Rmerge(I) obsRpim(I) allRrim(I) allΧ2Diffraction-IDNet I/σ(I)
1.75-30654523.70.0330.020.0391.009134.82
2.16-30351737.30.0920.0360.099216.46
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2Diffraction-ID% possible all
1.75-1.813.10.4392.1364050.8240.2850.5250.681198.1
2.16-2.245.60.6612.0833580.810.2920.7251.066295.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
Blu-Icedata collection
HKL-2000data scaling
HKL-2000data reduction
PHENIX1.12_2829phasing
RefinementMethod to determine structure: SAD / Resolution: 1.75→29.52 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.959 / SU B: 4.567 / SU ML: 0.064 / Cross valid method: THROUGHOUT / ESU R: 0.168 / ESU R Free: 0.099
RfactorNum. reflection% reflectionSelection details
Rfree0.19466 3326 5.1 %RANDOM
Rwork0.16933 ---
obs0.1706 62103 99.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 43.475 Å2
Baniso -1Baniso -2Baniso -3
1-0.74 Å20 Å2-0.3 Å2
2---0.62 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.75→29.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4704 0 0 351 5055
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0124838
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3811.6396566
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7125598
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.80521.181237
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.90915858
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7181539
X-RAY DIFFRACTIONr_chiral_restr0.1020.2617
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023674
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_it5.4783.8912401
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it6.6585.832996
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it7.0844.5732437
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined8.58654.877521
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr4.08734838
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 254 -
Rwork0.289 4289 -
obs--94.37 %

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