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- PDB-8z62: Crystal structure of rRNA (uracil-C5)-methyltransferase from Pyro... -

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Basic information

Entry
Database: PDB / ID: 8z62
TitleCrystal structure of rRNA (uracil-C5)-methyltransferase from Pyrococcus horikoshii OT3
Components23S rRNA (uracil(747)-C(5))-methyltransferase
KeywordsTRANSFERASE / archaea / aromatic stacking / hinge movement / horizontal gene transfer / iron-sulfur protein / substrate selectivity
Function / homology
Function and homology information


23S rRNA (uracil747-C5)-methyltransferase / rRNA (uridine-C5-)-methyltransferase activity / rRNA methylation / 4 iron, 4 sulfur cluster binding / metal ion binding
Similarity search - Function
: / tRNA (uracil(54)-C(5))-methyltransferase, TRAM domain / RNA methyltransferase TrmA, conserved site / RNA methyltransferase trmA family signature 2. / (Uracil-5)-methyltransferase family / tRNA (Uracil-5-)-methyltransferase / SAM-dependent methyltransferase RNA m(5)U-type domain profile. / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / 23S rRNA (uracil(747)-C(5))-methyltransferase
Similarity search - Component
Biological speciesPyrococcus horikoshii OT3 (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsSaha, S. / Kanaujia, S.P.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)BT/PR51982/NER/95/2011/2023 India
CitationJournal: Biochemistry / Year: 2024
Title: Decoding Substrate Selectivity of an Archaeal RlmCD-like Methyltransferase Through Its Salient Traits.
Authors: Saha, S. / Kanaujia, S.P.
History
DepositionApr 18, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 16, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 23S rRNA (uracil(747)-C(5))-methyltransferase
B: 23S rRNA (uracil(747)-C(5))-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,27614
Polymers94,3212
Non-polymers95512
Water1,982110
1
A: 23S rRNA (uracil(747)-C(5))-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,88010
Polymers47,1611
Non-polymers7209
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 23S rRNA (uracil(747)-C(5))-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,3964
Polymers47,1611
Non-polymers2353
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.890, 96.610, 122.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein 23S rRNA (uracil(747)-C(5))-methyltransferase / 23S rRNA(m5U747)-methyltransferase


Mass: 47160.621 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii OT3 (archaea) / Strain: OT3 / Gene: PH1259 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Rosetta
References: UniProt: O58994, 23S rRNA (uracil747-C5)-methyltransferase

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Non-polymers , 5 types, 122 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY

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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: 2.32 Å3/Da / Density % sol: 47 % / Description: Orthorhombic
Crystal growTemperature: 293 K / Method: microbatch / pH: 7.5
Details: 0.1 M HEPES sodium pH 7.5, 2% (v/v) PEG 400, 2.0 M ammounium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Apr 15, 2023 / Details: Vari Max
RadiationMonochromator: Nickel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.2→96.61 Å / Num. obs: 18612 / % possible obs: 100 % / Redundancy: 8 % / CC1/2: 0.986 / Rmerge(I) obs: 0.224 / Rpim(I) all: 0.083 / Rrim(I) all: 0.239 / Χ2: 0.94 / Net I/σ(I): 8.3 / Num. measured all: 149497
Reflection shellResolution: 3.2→3.42 Å / % possible obs: 100 % / Redundancy: 8.1 % / Rmerge(I) obs: 0.536 / Num. measured all: 26915 / Num. unique obs: 3314 / CC1/2: 0.898 / Rpim(I) all: 0.198 / Rrim(I) all: 0.572 / Χ2: 0.76 / Net I/σ(I) obs: 3.5

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Processing

Software
NameVersionClassification
HKL-30003000data collection
MOSFLM7.4.0data reduction
Aimless0.7.13data scaling
PHASER2.8.3phasing
REFMAC5.8.0352refinement
Coot0.9.8.92model building
PDB_EXTRACT4.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AF-O58994-F1

Resolution: 3.2→75.83 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.88 / SU B: 41.261 / SU ML: 0.352 / Cross valid method: THROUGHOUT / ESU R Free: 0.48 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23723 928 5 %RANDOM
Rwork0.16916 ---
obs0.17247 17639 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.149 Å2
Baniso -1Baniso -2Baniso -3
1--2.4 Å2-0 Å20 Å2
2--2.95 Å2-0 Å2
3----0.55 Å2
Refinement stepCycle: 1 / Resolution: 3.2→75.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6610 0 59 110 6779
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0126836
X-RAY DIFFRACTIONr_bond_other_d0.0010.0166702
X-RAY DIFFRACTIONr_angle_refined_deg1.4071.6589210
X-RAY DIFFRACTIONr_angle_other_deg0.4341.57215441
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5095824
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.88555
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.242101241
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0560.21001
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.027926
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021606
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_it2.4342.7033284
X-RAY DIFFRACTIONr_mcbond_other2.4342.7033284
X-RAY DIFFRACTIONr_mcangle_it4.0424.8534103
X-RAY DIFFRACTIONr_mcangle_other4.0424.8524104
X-RAY DIFFRACTIONr_scbond_it2.8823.0343552
X-RAY DIFFRACTIONr_scbond_other2.8813.0353553
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.8825.425105
X-RAY DIFFRACTIONr_long_range_B_refined7.29326.337338
X-RAY DIFFRACTIONr_long_range_B_other7.29326.337336
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.2→3.283 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 62 -
Rwork0.229 1283 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.679-0.41530.09321.03630.11860.7853-0.10450.1657-0.20010.01790.06450.0771-0.01040.02690.040.062-0.00040.02630.0344-0.0040.1464-9.96910.6471-13.3034
22.12150.0947-0.16242.0129-0.10931.5555-0.02530.08160.0784-0.00280.08230.41060.1841-0.3178-0.0570.0339-0.04030.02220.11620.06520.1924-28.988636.0512-39.8575
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 412
2X-RAY DIFFRACTION2B3 - 412

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