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- PDB-8x4p: Crystal structure of the Y135A mutant of DIMT1 in complex with ad... -

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Basic information

Entry
Database: PDB / ID: 8x4p
TitleCrystal structure of the Y135A mutant 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 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
SINEFUNGIN / Probable ribosomal RNA small subunit methyltransferase A
Similarity search - Component
Biological speciesPyrococcus horikoshii OT3 (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 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)67,5708
Polymers66,5462
Non-polymers1,0246
Water1,838102
1
A: Probable ribosomal RNA small subunit methyltransferase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9166
Polymers33,2731
Non-polymers6435
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-24 kcal/mol
Surface area13470 Å2
MethodPISA
2
B: Probable ribosomal RNA small subunit methyltransferase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6542
Polymers33,2731
Non-polymers3811
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area13470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.060, 79.960, 85.410
Angle α, β, γ (deg.)90.00, 116.28, 90.00
Int Tables number5
Space group name H-MC121

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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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / 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: 2.55 Å3/Da / Density % sol: 51.76 % / 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: Oct 7, 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: 2.6→76.58 Å / Num. obs: 20945 / % possible obs: 94.3 % / Redundancy: 4.4 % / CC1/2: 0.939 / Rmerge(I) obs: 0.19 / Rpim(I) all: 0.104 / Rrim(I) all: 0.218 / Χ2: 0.98 / Net I/σ(I): 5.8 / Num. measured all: 91861
Reflection shellResolution: 2.6→2.72 Å / % possible obs: 82.1 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.566 / Num. measured all: 9752 / Num. unique obs: 2200 / CC1/2: 0.846 / Rpim(I) all: 0.3 / Rrim(I) all: 0.643 / Χ2: 0.78 / 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: 2.6→76.58 Å / Cor.coef. Fo:Fc: 0.852 / Cor.coef. Fo:Fc free: 0.873 / SU B: 33.949 / SU ML: 0.35 / Cross valid method: THROUGHOUT / ESU R: 1.172 / ESU R Free: 0.374 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28909 1058 5.1 %RANDOM
Rwork0.26232 ---
obs0.26369 19804 93.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 52.758 Å2
Baniso -1Baniso -2Baniso -3
1-1.88 Å2-0 Å22.19 Å2
2---1.9 Å2-0 Å2
3----1.44 Å2
Refinement stepCycle: 1 / Resolution: 2.6→76.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4376 0 58 102 4536
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0124514
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164432
X-RAY DIFFRACTIONr_angle_refined_deg1.5671.6446080
X-RAY DIFFRACTIONr_angle_other_deg0.5181.56810330
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.4115538
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.634534
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.30110884
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.070.2690
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024958
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02852
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_it2.212.4512164
X-RAY DIFFRACTIONr_mcbond_other2.1832.452164
X-RAY DIFFRACTIONr_mcangle_it3.6593.6612698
X-RAY DIFFRACTIONr_mcangle_other3.6643.6632699
X-RAY DIFFRACTIONr_scbond_it1.8812.6172350
X-RAY DIFFRACTIONr_scbond_other1.8792.6172350
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.1033.8593383
X-RAY DIFFRACTIONr_long_range_B_refined6.33334.1515068
X-RAY DIFFRACTIONr_long_range_B_other6.33334.1515068
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 88 -
Rwork0.334 1554 -
obs--99.15 %
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)
12.64271.0623-0.84741.9802-0.86070.4859-0.02120.0026-0.1345-0.11340.08320.09980.0463-0.0118-0.06190.64570.00340.02370.013-0.02220.13468.4121-17.597830.4928
20.493-0.13630.63771.821-1.30472.1053-0.0732-0.01880.04590.08270.10310.2278-0.1251-0.0405-0.02990.57820.03690.02320.01240.00740.133322.1101-25.37892.733
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A21 - 290
2X-RAY DIFFRACTION2B21 - 290

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