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- PDB-8x4o: Crystal structure of the Y135A mutant of DIMT1 in complex with 5'... -

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Basic information

Entry
Database: PDB / ID: 8x4o
TitleCrystal structure of the Y135A mutant of DIMT1 in complex with 5'-methylthioadenosine 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
5'-DEOXY-5'-METHYLTHIOADENOSINE / Probable ribosomal RNA small subunit methyltransferase A
Similarity search - Component
Biological speciesPyrococcus horikoshii OT3 (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 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

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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)67,3968
Polymers66,5462
Non-polymers8506
Water37821
1
A: Probable ribosomal RNA small subunit methyltransferase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6984
Polymers33,2731
Non-polymers4253
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area80 Å2
ΔGint-19 kcal/mol
Surface area13980 Å2
MethodPISA
2
B: Probable ribosomal RNA small subunit methyltransferase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6984
Polymers33,2731
Non-polymers4253
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area80 Å2
ΔGint-19 kcal/mol
Surface area13980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.539, 125.539, 37.140
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number143
Space group name H-MP3

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Components

#1: Protein Probable ribosomal RNA small subunit methyltransferase A


Mass: 33273.023 Da / Num. of mol.: 2 / Mutation: Y135A
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
#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.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Formula: H2O
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: 2.36 Å3/Da / Density % sol: 47.97 % / Description: Primitive Trigonal
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: Oct 6, 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: 3→62.85 Å / Num. obs: 12475 / % possible obs: 94.9 % / Redundancy: 6.1 % / CC1/2: 0.995 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.044 / Rrim(I) all: 0.107 / Χ2: 0.87 / Net I/σ(I): 9.8
Reflection shellResolution: 3→3.18 Å / % possible obs: 100 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.454 / Num. measured all: 13062 / Num. unique obs: 2148 / CC1/2: 0.915 / Rpim(I) all: 0.201 / Rrim(I) all: 0.497 / Χ2: 0.7 / Net I/σ(I) obs: 3.4

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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: 3→62.85 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.861 / SU B: 60.871 / SU ML: 0.542 / Cross valid method: THROUGHOUT / ESU R Free: 0.593 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30437 971 7.8 %RANDOM
Rwork0.21949 ---
obs0.22609 11496 94.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 113.586 Å2
Baniso -1Baniso -2Baniso -3
1-1.65 Å20.82 Å20 Å2
2--1.65 Å20 Å2
3----5.35 Å2
Refinement stepCycle: 1 / Resolution: 3→62.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4364 0 50 21 4435
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0124494
X-RAY DIFFRACTIONr_bond_other_d0.0240.0164418
X-RAY DIFFRACTIONr_angle_refined_deg1.1341.6456048
X-RAY DIFFRACTIONr_angle_other_deg0.8261.56710290
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.3565536
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.672534
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.67510882
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0540.2684
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024936
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02850
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_it3.6916.8992150
X-RAY DIFFRACTIONr_mcbond_other3.6886.8992150
X-RAY DIFFRACTIONr_mcangle_it6.09510.3332684
X-RAY DIFFRACTIONr_mcangle_other6.09410.3352685
X-RAY DIFFRACTIONr_scbond_it3.6137.2242344
X-RAY DIFFRACTIONr_scbond_other3.6127.2262345
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.0510.713365
X-RAY DIFFRACTIONr_long_range_B_refined10.4815239
X-RAY DIFFRACTIONr_long_range_B_other10.485240
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.39 86 -
Rwork0.298 903 -
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)
15.07260.73282.74580.91930.02833.96550.13560.0204-0.2044-0.1222-0.3029-0.32710.06750.89550.16720.03730.04130.08490.51070.11270.462140.2995-16.3377-6.2798
22.665-2.27631.42973.5968-2.45613.9913-0.2337-0.1034-0.3951-0.20070.06840.00890.82860.42150.16530.44390.20450.13180.1289-0.01310.48246.0051-43.0659-6.2866
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A22 - 290
2X-RAY DIFFRACTION2B22 - 290

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