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- PDB-8x46: Crystal structure of DIMT1 in complex with adenosylornithine (SFG... -

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Basic information

Entry
Database: PDB / ID: 8x46
TitleCrystal structure of DIMT1 in complex with adenosylornithine (SFG) from Pyrococcus horikoshii
ComponentsProbable ribosomal RNA small subunit methyltransferase A
KeywordsTRANSFERASE / Archaea / KsgA/DIMT1 / rRNA methyltransferase / SAM / SAH / SFG
Function / homology
Function and homology information


rRNA (adenine-N6,N6-)-dimethyltransferase activity / Transferases; Transferring one-carbon groups; Methyltransferases / RNA binding / cytoplasm
Similarity search - Function
rRNA adenine dimethylase-like, C-terminal / Ribosomal RNA adenine dimethylase / Ribosomal RNA adenine methylase transferase, conserved site / Ribosomal RNA adenine methylase transferase, N-terminal / Ribosomal RNA adenine dimethylases signature. / Ribosomal RNA adenine dimethylases / Ribosomal RNA adenine methyltransferase KsgA/Erm / Ribosomal RNA adenine dimethylase / rRNA adenine N(6)-methyltransferase family profile. / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
ARGININE / DI(HYDROXYETHYL)ETHER / SINEFUNGIN / SULFITE ION / Probable ribosomal RNA small subunit methyltransferase A
Similarity search - Component
Biological speciesPyrococcus horikoshii OT3 (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsSaha, S. / Kanaujia, S.P.
Funding support India, 1items
OrganizationGrant numberCountry
Science and Engineering Research Board (SERB)EEQ/2021/000060 India
CitationJournal: Structure / Year: 2024
Title: Structural and functional characterization of archaeal DIMT1 unveils distinct protein dynamics essential for efficient catalysis.
Authors: Saha, S. / Kanaujia, S.P.
History
DepositionNov 15, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 28, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Database references / Structure summary / Category: citation / pdbx_entry_details
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable ribosomal RNA small subunit methyltransferase A
B: Probable ribosomal RNA small subunit methyltransferase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,66118
Polymers66,7302
Non-polymers1,93116
Water4,234235
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3580 Å2
ΔGint-208 kcal/mol
Surface area24360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.150, 80.340, 84.110
Angle α, β, γ (deg.)90.00, 115.46, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Probable ribosomal RNA small subunit methyltransferase A


Mass: 33365.117 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii OT3 (archaea) / Strain: OT3 / Gene: DIMT1 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Rosetta
References: UniProt: O59487, 16S rRNA (adenine1518-N6/adenine1519-N6)-dimethyltransferase

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Non-polymers , 8 types, 251 molecules

#2: Chemical ChemComp-SFG / SINEFUNGIN / ADENOSYL-ORNITHINE


Mass: 381.387 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H23N7O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-ARG / ARGININE


Type: L-peptide linking / Mass: 175.209 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H15N4O2
#7: Chemical ChemComp-SO3 / SULFITE ION


Mass: 80.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO3
#8: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 235 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.54 Å3/Da / Density % sol: 51.62 % / Description: C-centered Monoclinic
Crystal growTemperature: 293 K / Method: microbatch / pH: 6.5
Details: 0.2 M Zinc Acetate Dihydrate, 0.1 M Sodium Cacodylate Trihydrate pH 6.5, 18% (w/v) PEG 8000

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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: May 16, 2022 / Details: VariMax HF
RadiationMonochromator: Nickel filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→75.94 Å / Num. obs: 36508 / % possible obs: 100 % / Redundancy: 4.4 % / CC1/2: 0.994 / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.059 / Rrim(I) all: 0.126 / Χ2: 0.58 / Net I/σ(I): 6.3 / Num. measured all: 161859
Reflection shellResolution: 2.2→2.27 Å / % possible obs: 100 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.554 / Num. measured all: 13702 / Num. unique obs: 3157 / CC1/2: 0.866 / Rpim(I) all: 0.302 / Rrim(I) all: 0.633 / Χ2: 0.57 / Net I/σ(I) obs: 2

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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_EXTRACT4.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→64.45 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.918 / SU B: 16.223 / SU ML: 0.207 / Cross valid method: THROUGHOUT / ESU R: 0.26 / ESU R Free: 0.215 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26103 1759 4.8 %RANDOM
Rwork0.21301 ---
obs0.21535 34748 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.284 Å2
Baniso -1Baniso -2Baniso -3
1-2.72 Å2-0 Å20.1 Å2
2---1.75 Å2-0 Å2
3----0.73 Å2
Refinement stepCycle: 1 / Resolution: 2.2→64.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4378 0 108 235 4721
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0124564
X-RAY DIFFRACTIONr_bond_other_d0.0020.0164482
X-RAY DIFFRACTIONr_angle_refined_deg1.421.6466137
X-RAY DIFFRACTIONr_angle_other_deg0.5181.56910444
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4975538
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.717536
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.54310891
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.070.2692
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024997
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02865
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_it1.9492.522164
X-RAY DIFFRACTIONr_mcbond_other1.9472.522164
X-RAY DIFFRACTIONr_mcangle_it3.0693.7672695
X-RAY DIFFRACTIONr_mcangle_other3.073.7672696
X-RAY DIFFRACTIONr_scbond_it2.6092.8962400
X-RAY DIFFRACTIONr_scbond_other2.6082.8962401
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.2394.1783442
X-RAY DIFFRACTIONr_long_range_B_refined6.9737.5275233
X-RAY DIFFRACTIONr_long_range_B_other6.937.1645196
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 132 -
Rwork0.302 2562 -
obs--99.96 %
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)
10.18120.09610.47942.1171.20571.8134-0.08120.02250.0614-0.2861-0.0339-0.1799-0.22020.02940.1150.2369-0.02660.04860.00720.0080.066219.48693.297434.7629
21.526-0.8173-0.44742.37050.47940.1822-0.00440.0427-0.22340.3088-0.05650.04240.0207-0.01050.06090.16580.00720.06910.0070.01180.107432.202510.92698.1212
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A22 - 290
2X-RAY DIFFRACTION2B22 - 290

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