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- PDB-8h27: Crystal structure of MnmM from S. aureus complexed with SAM (2.04 A) -

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Basic information

Entry
Database: PDB / ID: 8h27
TitleCrystal structure of MnmM from S. aureus complexed with SAM (2.04 A)
Components16S rRNA (Cytosine(1402)-N(4))-methyltransferase
KeywordsTRANSFERASE / Methyltrnasferase tRNA post-transcriptional modification MnmC mnm5(s2)U
Function / homologytRNA 5-(aminomethyl)-2-thiouridylate-methyltransferase / Putative rRNA methylase / Putative rRNA methylase / tRNA processing / methyltransferase activity / methylation / S-adenosyl-L-methionine-dependent methyltransferase superfamily / S-ADENOSYLMETHIONINE / tRNA (mnm(5)s(2)U34)-methyltransferase
Function and homology information
Biological speciesStaphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04 Å
AuthorsKim, J. / Cho, G. / Lee, J.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
CitationJournal: Nucleic Acids Res. / Year: 2023
Title: Identification of a novel 5-aminomethyl-2-thiouridine methyltransferase in tRNA modification.
Authors: Cho, G. / Lee, J. / Kim, J.
History
DepositionOct 5, 2022Deposition site: PDBJ / Processing site: PDBE
Revision 1.0Jan 25, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 22, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2May 1, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 16S rRNA (Cytosine(1402)-N(4))-methyltransferase
B: 16S rRNA (Cytosine(1402)-N(4))-methyltransferase
C: 16S rRNA (Cytosine(1402)-N(4))-methyltransferase
D: 16S rRNA (Cytosine(1402)-N(4))-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,2585
Polymers87,8604
Non-polymers3981
Water6,395355
1
A: 16S rRNA (Cytosine(1402)-N(4))-methyltransferase
C: 16S rRNA (Cytosine(1402)-N(4))-methyltransferase


Theoretical massNumber of molelcules
Total (without water)43,9302
Polymers43,9302
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2680 Å2
ΔGint-18 kcal/mol
Surface area17120 Å2
MethodPISA
2
B: 16S rRNA (Cytosine(1402)-N(4))-methyltransferase
D: 16S rRNA (Cytosine(1402)-N(4))-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,3283
Polymers43,9302
Non-polymers3981
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2820 Å2
ΔGint-14 kcal/mol
Surface area15940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.015, 114.015, 67.009
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein
16S rRNA (Cytosine(1402)-N(4))-methyltransferase / rRNA methylase YtqB


Mass: 21964.928 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
Strain: NCTC 8325 / PS 47 / Gene: SAOUHSC_01878 / Plasmid: pLATE31 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q2FXG9
#2: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE / S-Adenosyl methionine


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 355 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.69 Å3/Da / Density % sol: 54.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M lithium sulfate monohydrate, 0.1 M BIS-TRIS pH 6.5, and 25% w/v PEG3350

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: LN2 / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.97949 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 29, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.04→43.46 Å / Num. obs: 46406 / % possible obs: 84.6 % / Redundancy: 13.9 % / Biso Wilson estimate: 40.76 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.03 / Rrim(I) all: 0.112 / Net I/σ(I): 17.8
Reflection shellResolution: 2.04→2.23 Å / Redundancy: 14.6 % / Rmerge(I) obs: 2.271 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 4642 / CC1/2: 0.627 / Rpim(I) all: 0.615 / Rrim(I) all: 2.353 / % possible all: 36.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
MxDCdata collection
XDSJan 10, 2022data reduction
STARANISOdata scaling
MOLREP11.9.02phasing
Coot0.9.8.3model building
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold model (UniProt: Q2FXG9)

Resolution: 2.04→43.46 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.945 / SU B: 10.812 / SU ML: 0.143 / Cross valid method: THROUGHOUT / ESU R: 0.227 / ESU R Free: 0.181 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.22359 2248 4.8 %RANDOM
Rwork0.18887 ---
obs0.19058 44157 84.57 %-
Solvent computationIon probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.3 Å / Solvent model: MASK
Displacement parametersBiso mean: 53.712 Å2
Baniso -1Baniso -2Baniso -3
1--0.21 Å20 Å20 Å2
2---0.21 Å20 Å2
3---0.42 Å2
Refinement stepCycle: LAST / Resolution: 2.04→43.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5635 0 27 355 6017
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0185774
X-RAY DIFFRACTIONr_bond_other_d0.0010.025500
X-RAY DIFFRACTIONr_angle_refined_deg1.3131.8677817
X-RAY DIFFRACTIONr_angle_other_deg1.0682.81612687
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1895701
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.71125286
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.357151015
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9111511
X-RAY DIFFRACTIONr_chiral_restr0.0820.2909
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026483
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021210
X-RAY DIFFRACTIONr_mcbond_it2.6763.0772840
X-RAY DIFFRACTIONr_mcbond_other2.6753.0772840
X-RAY DIFFRACTIONr_mcangle_it3.9714.593529
X-RAY DIFFRACTIONr_mcangle_other3.9714.5923530
X-RAY DIFFRACTIONr_scbond_it3.1813.4552934
X-RAY DIFFRACTIONr_scbond_other3.1813.4552934
X-RAY DIFFRACTIONr_scangle_other4.7725.054289
X-RAY DIFFRACTIONr_long_range_B_refined7.05537.4286192
X-RAY DIFFRACTIONr_long_range_B_other7.00136.9476110
LS refinement shellResolution: 2.041→2.094 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 11 -
Rwork0.253 260 -
obs--6.7 %
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)
11.0527-0.12820.2911.5634-0.58991.7268-0.0615-0.11120.13020.04690.07010.1510.0512-0.2518-0.00850.05840.0171-00.132-0.01310.034653.383-37.7855.08
22.5942-0.70571.11062.83210.47484.2528-0.1413-0.18090.21450.47440.1498-0.1887-0.13670.1565-0.00850.12670.0713-0.05750.1654-0.00140.144636.416-5.89920.035
30.9147-0.92640.22063.16720.11796.00530.13770.24550.4463-0.71980.0171-0.4676-0.46390.6699-0.15480.2915-0.03920.12440.33180.06540.266260.241-21.21-23.206
41.946-0.15810.69681.082-0.37962.93170.07010.0278-0.2038-0.0786-0.0306-0.10150.29410.264-0.03960.03510.0276-0.00410.0351-0.0080.062518.418-6.483-7.21
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 189
2X-RAY DIFFRACTION2B1 - 188
3X-RAY DIFFRACTION3C1 - 189
4X-RAY DIFFRACTION4D1 - 189

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