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- PDB-8x45: Crystal structure of DIMT1 in complex with 5'-methylthioadenosine... -

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Basic information

Entry
Database: PDB / ID: 8x45
TitleCrystal structure of DIMT1 in complex with 5'-methylthioadenosine from Pyrococcus horikoshii (FormII)
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 dimethylases signature. / Ribosomal RNA adenine methylase transferase, N-terminal / 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
ACETATE ION / 5'-DEOXY-5'-METHYLTHIOADENOSINE / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / SULFITE ION / Probable ribosomal RNA small subunit methyltransferase A
Similarity search - Component
Biological speciesPyrococcus horikoshii OT3 (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 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)68,66621
Polymers66,7302
Non-polymers1,93619
Water2,738152
1
A: Probable ribosomal RNA small subunit methyltransferase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,47712
Polymers33,3651
Non-polymers1,11211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Probable ribosomal RNA small subunit methyltransferase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1899
Polymers33,3651
Non-polymers8248
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)120.740, 80.230, 85.710
Angle α, β, γ (deg.)90.00, 116.17, 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 , 9 types, 171 molecules

#2: Chemical ChemComp-MTA / 5'-DEOXY-5'-METHYLTHIOADENOSINE


Mass: 297.334 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H15N5O3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-SO3 / SULFITE ION


Mass: 80.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO3
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / 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-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 152 / 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: 2.6 Å3/Da / Density % sol: 52.8 % / Description: C-cetered Monoclinic
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.4 / Details: 0.2 M Zinc Acetate Dihydrate, 20% (w/v) PEG 3350

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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 23, 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: 2.5→76.92 Å / Num. obs: 24312 / % possible obs: 95.2 % / Redundancy: 4.1 % / CC1/2: 0.987 / Rmerge(I) obs: 0.131 / Rpim(I) all: 0.075 / Rrim(I) all: 0.152 / Χ2: 0.91 / Net I/σ(I): 7.1 / Num. measured all: 99968
Reflection shellResolution: 2.5→2.6 Å / % possible obs: 100 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.704 / Num. measured all: 11723 / Num. unique obs: 2847 / CC1/2: 0.778 / Rpim(I) all: 0.39 / Rrim(I) all: 0.808 / Χ2: 0.63 / Net I/σ(I) obs: 2.1

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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: 2.5→76.92 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.883 / SU B: 24.634 / SU ML: 0.284 / Cross valid method: THROUGHOUT / ESU R: 0.607 / ESU R Free: 0.327 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28213 1178 4.9 %RANDOM
Rwork0.23109 ---
obs0.23364 23099 95.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.118 Å2
Baniso -1Baniso -2Baniso -3
1-2.75 Å2-0 Å2-0.27 Å2
2---1.5 Å2-0 Å2
3----0.67 Å2
Refinement stepCycle: 1 / Resolution: 2.5→76.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4384 0 109 152 4645
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0124568
X-RAY DIFFRACTIONr_bond_other_d0.0040.0164487
X-RAY DIFFRACTIONr_angle_refined_deg1.5461.6466129
X-RAY DIFFRACTIONr_angle_other_deg0.5091.56610452
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9195539
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.431534
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.43110886
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0690.2690
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024974
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02860
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_it2.6853.1192157
X-RAY DIFFRACTIONr_mcbond_other2.6853.1172156
X-RAY DIFFRACTIONr_mcangle_it4.2114.6642692
X-RAY DIFFRACTIONr_mcangle_other4.2154.6662693
X-RAY DIFFRACTIONr_scbond_it3.1483.5012411
X-RAY DIFFRACTIONr_scbond_other3.1483.5032412
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.9965.0693437
X-RAY DIFFRACTIONr_long_range_B_refined7.61345.2515075
X-RAY DIFFRACTIONr_long_range_B_other7.62245.2175062
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.365 95 -
Rwork0.314 1764 -
obs--99.95 %
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)
10.5153-0.03120.6542.36530.9861.9434-0.12710.03620.0473-0.17260.0652-0.1189-0.04270.02680.06190.1583-0.06060.03630.0421-0.01220.025919.070618.36435.5339
21.8695-0.3872-0.39182.19230.46660.28110.0104-0.0142-0.16480.17380.04490.0459-0.0796-0.0123-0.05530.11670.03470.08390.02850.03010.085332.639726.16368.0734
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A21 - 290
2X-RAY DIFFRACTION2B22 - 290

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