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- PDB-8x4g: Crystal structure of the D117A mutant of DIMT1 from Pyrococcus ho... -

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Basic information

Entry
Database: PDB / ID: 8x4g
TitleCrystal structure of the D117A mutant of DIMT1 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
Probable ribosomal RNA small subunit methyltransferase A
Similarity search - Component
Biological speciesPyrococcus horikoshii OT3 (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.3 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.page_last

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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


Theoretical massNumber of molelcules
Total (without water)66,6422
Polymers66,6422
Non-polymers00
Water23413
1
A: Probable ribosomal RNA small subunit methyltransferase A


Theoretical massNumber of molelcules
Total (without water)33,3211
Polymers33,3211
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Probable ribosomal RNA small subunit methyltransferase A


Theoretical massNumber of molelcules
Total (without water)33,3211
Polymers33,3211
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)118.170, 80.630, 84.820
Angle α, β, γ (deg.)90.00, 114.86, 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: 33321.109 Da / Num. of mol.: 2 / Mutation: D117A
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Formula: H2O
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: 2.56 Å3/Da / Density % sol: 52.04 % / 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: Sep 2, 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: 3.3→76.96 Å / Num. obs: 10317 / % possible obs: 93.6 % / Redundancy: 4.6 % / CC1/2: 0.954 / Rmerge(I) obs: 0.203 / Rpim(I) all: 0.107 / Rrim(I) all: 0.23 / Χ2: 0.96 / Net I/σ(I): 6.1 / Num. measured all: 47267
Reflection shellResolution: 3.3→3.56 Å / % possible obs: 87.7 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.278 / Num. measured all: 9214 / Num. unique obs: 1995 / CC1/2: 0.952 / Rpim(I) all: 0.143 / Rrim(I) all: 0.314 / Χ2: 0.79 / 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: 3.3→64.52 Å / Cor.coef. Fo:Fc: 0.837 / Cor.coef. Fo:Fc free: 0.78 / SU B: 71.834 / SU ML: 0.533 / Cross valid method: THROUGHOUT / ESU R Free: 0.721 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29883 1074 10.4 %RANDOM
Rwork0.2484 ---
obs0.25363 9242 93.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.841 Å2
Baniso -1Baniso -2Baniso -3
1-5.27 Å20 Å20.44 Å2
2---4.81 Å20 Å2
3----0.61 Å2
Refinement stepCycle: 1 / Resolution: 3.3→64.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4384 0 0 13 4397
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0124466
X-RAY DIFFRACTIONr_bond_other_d0.0040.0164396
X-RAY DIFFRACTIONr_angle_refined_deg1.3211.6446010
X-RAY DIFFRACTIONr_angle_other_deg0.4671.56610242
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.6665538
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.812534
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.25810884
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0580.2678
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024932
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_it1.530.2532158
X-RAY DIFFRACTIONr_mcbond_other1.530.2532158
X-RAY DIFFRACTIONr_mcangle_it2.3260.3722694
X-RAY DIFFRACTIONr_mcangle_other2.3260.3722695
X-RAY DIFFRACTIONr_scbond_it1.3160.2712308
X-RAY DIFFRACTIONr_scbond_other1.3160.2712309
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.8540.3953317
X-RAY DIFFRACTIONr_long_range_B_refined3.0222.8325043
X-RAY DIFFRACTIONr_long_range_B_other3.0212.8285043
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.3→3.386 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.36 88 -
Rwork0.305 737 -
obs--99.88 %
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)
10.51990.0350.52771.97290.81531.1931-0.04390.04880.0893-0.2279-0.0297-0.1699-0.24770.05310.07360.1582-0.0571-0.02210.3-0.00770.363419.321116.39835.5382
22.1997-0.5174-0.63772.25560.7080.468-0.0277-0.0198-0.26520.3515-0.0402-0.0182-0.0208-0.07140.06780.16180.0346-0.04590.29970.06930.30531.973824.18827.8499
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A21 - 290
2X-RAY DIFFRACTION2B21 - 290

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