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- PDB-8h26: Crystal structure of MnmM from S. aureus complexed with SAH (1.50 A) -

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Basic information

Entry
Database: PDB / ID: 8h26
TitleCrystal structure of MnmM from S. aureus complexed with SAH (1.50 A)
Components16S rRNA (Cytosine(1402)-N(4))-methyltransferase
KeywordsTRANSFERASE / Methyltrnasferase tRNA post-transcriptional modification MnmC mnm5(s2)U
Function / homology
Function and homology information


tRNA 5-(aminomethyl)-2-thiouridylate-methyltransferase / tRNA processing / methyltransferase activity / methylation
Similarity search - Function
Putative rRNA methylase / Putative rRNA methylase / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / tRNA (mnm(5)s(2)U34)-methyltransferase
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsKim, J. / Cho, G. / Lee, J.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
CitationJournal: To Be Published
Title: Crystal structure of MnmM from S. aureus complexed with SAH (1.50 A)
Authors: Kim, J. / Cho, G. / Lee, J.
History
DepositionOct 5, 2022Deposition site: PDBJ / Processing site: PDBE
Revision 1.0Jan 18, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
E: 16S rRNA (Cytosine(1402)-N(4))-methyltransferase
F: 16S rRNA (Cytosine(1402)-N(4))-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,32710
Polymers131,7906
Non-polymers1,5384
Water12,214678
1
A: 16S rRNA (Cytosine(1402)-N(4))-methyltransferase
E: 16S rRNA (Cytosine(1402)-N(4))-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,3143
Polymers43,9302
Non-polymers3841
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2930 Å2
ΔGint-12 kcal/mol
Surface area15050 Å2
MethodPISA
2
B: 16S rRNA (Cytosine(1402)-N(4))-methyltransferase
C: 16S rRNA (Cytosine(1402)-N(4))-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,6994
Polymers43,9302
Non-polymers7692
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2930 Å2
ΔGint-12 kcal/mol
Surface area15710 Å2
MethodPISA
3
D: 16S rRNA (Cytosine(1402)-N(4))-methyltransferase
F: 16S rRNA (Cytosine(1402)-N(4))-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,3143
Polymers43,9302
Non-polymers3841
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2770 Å2
ΔGint-14 kcal/mol
Surface area15290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.329, 69.362, 74.608
Angle α, β, γ (deg.)91.25, 112.97, 114.05
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 21964.928 Da / Num. of mol.: 6
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-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C14H20N6O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 678 / 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: 2.01 Å3/Da / Density % sol: 38.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 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: 1.5→67.09 Å / Num. obs: 104221 / % possible obs: 92.7 % / Redundancy: 7.3 % / Biso Wilson estimate: 21.6 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.028 / Rrim(I) all: 0.074 / Net I/σ(I): 14.7
Reflection shellResolution: 1.5→1.68 Å / Redundancy: 7.4 % / Rmerge(I) obs: 1.285 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 5203 / CC1/2: 0.637 / Rpim(I) all: 0.507 / Rrim(I) all: 1.382 / % possible all: 72.3

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Processing

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

Resolution: 1.5→67.09 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.944 / SU B: 4.95 / SU ML: 0.084 / Cross valid method: THROUGHOUT / ESU R: 0.125 / ESU R Free: 0.119 / 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
Rfree0.21855 5112 4.9 %RANDOM
Rwork0.18281 ---
obs0.18451 98695 63.35 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.373 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20.04 Å20.02 Å2
2--0.51 Å20.01 Å2
3----0.53 Å2
Refinement stepCycle: LAST / Resolution: 1.5→67.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8298 0 104 678 9080
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0188705
X-RAY DIFFRACTIONr_bond_other_d0.0020.028253
X-RAY DIFFRACTIONr_angle_refined_deg1.6521.86511808
X-RAY DIFFRACTIONr_angle_other_deg1.2072.81219050
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.64151062
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.24224.953430
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.909151528
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3721518
X-RAY DIFFRACTIONr_chiral_restr0.1180.21371
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.029861
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021847
X-RAY DIFFRACTIONr_mcbond_it2.1321.5054263
X-RAY DIFFRACTIONr_mcbond_other2.131.5054263
X-RAY DIFFRACTIONr_mcangle_it3.1492.2335320
X-RAY DIFFRACTIONr_mcangle_other3.152.2345321
X-RAY DIFFRACTIONr_scbond_it2.9421.9024442
X-RAY DIFFRACTIONr_scbond_other2.9421.9024442
X-RAY DIFFRACTIONr_scangle_other4.4812.7256489
X-RAY DIFFRACTIONr_long_range_B_refined7.0520.0739594
X-RAY DIFFRACTIONr_long_range_B_other7.01319.5199439
LS refinement shellResolution: 1.502→1.541 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 16 -
Rwork0.297 230 -
obs--2.03 %
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)
12.496-0.89350.71162.58550.43961.733-0.11670.02390.2865-0.07920.0741-0.0786-0.380.10790.04260.0902-0.0291-0.00630.0140.00910.1109-23.67-12.28919.363
22.4468-1.0547-0.14022.9863-0.0291.77020.04310.12110.0164-0.229-0.09480.04350.0138-0.08780.05170.0360.0138-0.02130.0149-0.01330.047-11.0621.761-1.387
31.7543-0.32050.20383.62430.24681.38890.0417-0.0051-0.0635-0.2151-0.0675-0.10570.01960.06510.02580.01630.00590.01430.00520.00490.04964.464-6.1843.311
41.732-0.220.3543.652-0.50861.9541-0.0574-0.01110.05880.1930.04740.1667-0.233-0.15480.010.08060.05380.01030.03860.0030.017119.2235.267-24.411
52.02140.41380.65633.31480.83411.92380.1579-0.1533-0.23040.3691-0.0062-0.20950.28590.05-0.15170.06860.0011-0.04780.01820.01030.0694-15.446-42.7723.861
61.3103-0.75370.09653.89630.21661.2964-0.0027-0.0141-0.1510.22030.0722-0.09770.0909-0.0855-0.06950.04720.0076-0.03860.0347-0.00910.076929.0565.086-22.865
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 187
2X-RAY DIFFRACTION2B1 - 187
3X-RAY DIFFRACTION3C1 - 188
4X-RAY DIFFRACTION4D1 - 188
5X-RAY DIFFRACTION5E1 - 189
6X-RAY DIFFRACTION6F1 - 187

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