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- PDB-8x3w: Crystal structure of DIMT1 from the thermophilic archaeon, Pyroco... -

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Basic information

Entry
Database: PDB / ID: 8x3w
TitleCrystal structure of DIMT1 from the thermophilic archaeon, 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
ACETATE ION / ARGININE / DI(HYDROXYETHYL)ETHER / SULFITE ION / Probable ribosomal RNA small subunit methyltransferase A
Similarity search - Component
Biological speciesPyrococcus horikoshii OT3 (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.01 Å
AuthorsSayan, S. / Mandal, S.K. / 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 14, 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)69,86538
Polymers66,7302
Non-polymers3,13436
Water6,089338
1
A: Probable ribosomal RNA small subunit methyltransferase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,14723
Polymers33,3651
Non-polymers1,78222
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)34,71815
Polymers33,3651
Non-polymers1,35214
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)117.860, 80.170, 84.640
Angle α, β, γ (deg.)90.00, 115.50, 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 / DIMT1


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: rsmA / 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, 374 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-SO3 / SULFITE ION


Mass: 80.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO3
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#8: Chemical ChemComp-ARG / ARGININE


Type: L-peptide linking / Mass: 175.209 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H15N4O2
#9: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 338 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 2.52 Å3/Da / Density % sol: 51.28 % / Description: C-centered Monoclinic
Crystal growTemperature: 293 K / Method: microbatch / 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: Jul 11, 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: 2.01→76.39 Å / Num. obs: 47378 / % possible obs: 99.9 % / Redundancy: 4.8 % / CC1/2: 0.995 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.051 / Rrim(I) all: 0.112 / Χ2: 0.88 / Net I/σ(I): 10.4 / Num. measured all: 225549
Reflection shellResolution: 2.01→2.06 Å / % possible obs: 98.8 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.563 / Num. measured all: 15354 / Num. unique obs: 3435 / CC1/2: 0.727 / Rpim(I) all: 0.299 / Rrim(I) all: 0.639 / Χ2: 0.87 / Net I/σ(I) obs: 2.7

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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: 2.01→76.39 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.916 / SU B: 8.996 / SU ML: 0.132 / Cross valid method: THROUGHOUT / ESU R: 0.175 / ESU R Free: 0.166 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24559 2434 5.1 %RANDOM
Rwork0.19456 ---
obs0.19718 44943 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.853 Å2
Baniso -1Baniso -2Baniso -3
1-1.84 Å20 Å20.5 Å2
2---2.17 Å2-0 Å2
3----0.1 Å2
Refinement stepCycle: 1 / Resolution: 2.01→76.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4390 0 166 338 4894
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0124609
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164538
X-RAY DIFFRACTIONr_angle_refined_deg1.4551.6476158
X-RAY DIFFRACTIONr_angle_other_deg0.4671.56710573
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0645540
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.486536
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.88210893
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0640.2697
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024981
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02859
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_it2.0762.3192167
X-RAY DIFFRACTIONr_mcbond_other2.0722.3182167
X-RAY DIFFRACTIONr_mcangle_it3.1873.4592701
X-RAY DIFFRACTIONr_mcangle_other3.193.4592702
X-RAY DIFFRACTIONr_scbond_it3.2622.8712442
X-RAY DIFFRACTIONr_scbond_other3.2142.8662440
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.0314.0843457
X-RAY DIFFRACTIONr_long_range_B_refined7.4840.9575335
X-RAY DIFFRACTIONr_long_range_B_other7.41440.575267
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.01→2.062 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 192 -
Rwork0.268 3240 -
obs--98.73 %
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)
10.21970.01920.51260.37710.49051.7961-0.05320.00130.04610.0006-0.0155-0.0293-0.0522-0.040.06870.0602-0.0374-0.0020.0559-0.01590.019619.059517.815835.3058
21.422-0.294-0.40971.33830.18310.28180.00480.0181-0.08150.13410.0232-0.0075-0.034-0.0269-0.02790.02740.00170.00770.05040.02260.026531.583725.47787.8162
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A21 - 290
2X-RAY DIFFRACTION2B21 - 290

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