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- PDB-8x47: Crystal structure of DIMT1 in complex with S-adenosyl-L-homocyste... -

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Basic information

Entry
Database: PDB / ID: 8x47
TitleCrystal structure of DIMT1 in complex with S-adenosyl-L-homocysteine (SAH) 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 / TRIETHYLENE GLYCOL / S-ADENOSYL-L-HOMOCYSTEINE / SULFITE ION / Probable ribosomal RNA small subunit methyltransferase A
Similarity search - Component
Biological speciesPyrococcus horikoshii OT3 (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsSaha, S. / Dutta, A. / 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: Data collection / Database references / Structure summary
Category: chem_comp / citation / pdbx_entry_details
Item: _chem_comp.mon_nstd_flag / _chem_comp.type ..._chem_comp.mon_nstd_flag / _chem_comp.type / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,54610
Polymers33,3651
Non-polymers1,1819
Water63135
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area310 Å2
ΔGint-24 kcal/mol
Surface area13190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.990, 100.170, 77.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Probable ribosomal RNA small subunit methyltransferase A


Mass: 33365.117 Da / Num. of mol.: 1
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 , 9 types, 44 molecules

#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-SO3 / SULFITE ION


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


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#8: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#9: Chemical ChemComp-ARG / ARGININE


Type: L-peptide linking / Mass: 175.209 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15N4O2
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / 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: 2.24 Å3/Da / Density % sol: 45.03 % / Description: C-centered Orthorhombic
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 4, 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: 2.8→63.45 Å / Num. obs: 7997 / % possible obs: 98.1 % / Redundancy: 8.9 % / CC1/2: 0.991 / Rmerge(I) obs: 0.153 / Rpim(I) all: 0.056 / Rrim(I) all: 0.163 / Χ2: 1.09 / Net I/σ(I): 11.1 / Num. measured all: 71404
Reflection shellResolution: 2.8→2.95 Å / % possible obs: 96.7 % / Redundancy: 9.1 % / Rmerge(I) obs: 0.487 / Num. measured all: 10320 / Num. unique obs: 1135 / CC1/2: 0.95 / Rpim(I) all: 0.169 / Rrim(I) all: 0.516 / Χ2: 0.93 / Net I/σ(I) obs: 4.5

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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_EXTRACT4.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→63.45 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.885 / SU B: 27.294 / SU ML: 0.294 / Cross valid method: THROUGHOUT / ESU R Free: 0.431 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27596 384 4.8 %RANDOM
Rwork0.18433 ---
obs0.18886 7613 97.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 61.789 Å2
Baniso -1Baniso -2Baniso -3
1-6.38 Å20 Å2-0 Å2
2---3.69 Å20 Å2
3----2.69 Å2
Refinement stepCycle: 1 / Resolution: 2.8→63.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2156 0 71 35 2262
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0122261
X-RAY DIFFRACTIONr_bond_other_d0.0020.0162223
X-RAY DIFFRACTIONr_angle_refined_deg1.3891.6483030
X-RAY DIFFRACTIONr_angle_other_deg0.4381.5695180
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7695262
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.586518
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.66510438
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0610.2340
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022451
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02426
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_it3.634.4731060
X-RAY DIFFRACTIONr_mcbond_other3.6274.4731060
X-RAY DIFFRACTIONr_mcangle_it5.4946.6871318
X-RAY DIFFRACTIONr_mcangle_other5.4946.691319
X-RAY DIFFRACTIONr_scbond_it4.5175.0511201
X-RAY DIFFRACTIONr_scbond_other4.5155.0531202
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.0267.3451713
X-RAY DIFFRACTIONr_long_range_B_refined9.63170.6272539
X-RAY DIFFRACTIONr_long_range_B_other9.5970.692533
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.246 26 -
Rwork0.236 522 -
obs--95.97 %
Refinement TLS params.Method: refined / Origin x: 25.8643 Å / Origin y: 17.752 Å / Origin z: 5.7035 Å
111213212223313233
T0.0504 Å20.0338 Å20.0638 Å2-0.0945 Å2-0.0012 Å2--0.1358 Å2
L1.2206 °21.4041 °2-0.8547 °2-1.8064 °2-1.4509 °2--1.9451 °2
S-0.0754 Å °-0.0552 Å °-0.2062 Å °-0.119 Å °-0.1159 Å °-0.2094 Å °0.1784 Å °0.0915 Å °0.1913 Å °

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