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- PDB-9hmj: Crystal structure of MnmA from Streptococcus pneumoniae in comple... -

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Basic information

Entry
Database: PDB / ID: 9hmj
TitleCrystal structure of MnmA from Streptococcus pneumoniae in complex with ATP
ComponentstRNA-specific 2-thiouridylase MnmA
KeywordsTRANSFERASE / tRNA / tRNA thiolation / sulfur / sulfuration
Function / homology
Function and homology information


tRNA-uridine 2-sulfurtransferase / tRNA-uridine 2-sulfurtransferase activity / tRNA wobble position uridine thiolation / cytoplasm
Similarity search - Function
tRNA-specific 2-thiouridylase / tRNA-specific 2-thiouridylase MnmA-like, central domain superfamily / tRNA-specific 2-thiouridylase MnmA-like, central domain / tRNA-specific 2-thiouridylase MnmA-like, C-terminal domain / tRNA methyl transferase HUP domain / Aminomethyltransferase beta-barrel domain / tRNA methyl transferase PRC-barrel domain / Rossmann-like alpha/beta/alpha sandwich fold
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / DI(HYDROXYETHYL)ETHER / Chem-PG6 / tRNA-specific 2-thiouridylase MnmA
Similarity search - Component
Biological speciesStreptococcus pneumoniae TIGR4 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsGervason, S. / Pecqueur, L. / Golinelli-Pimpaneau, B.
Funding support France, 2items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-11-labx-0011 France
Agence Nationale de la Recherche (ANR)ANR-22-CE44-0012 France
CitationJournal: To Be Published
Title: A [4Fe-4S] cluster, coordinated by two conserved cysteines and one aspartate, is essential for tRNA thiolation by MnmA enzymes from two Gram positive bacteria
Authors: Golinelli-Pimpaneau, B.
History
DepositionDec 9, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 24, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: tRNA-specific 2-thiouridylase MnmA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,80213
Polymers41,8831
Non-polymers1,91912
Water5,080282
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, gel filtration + SEC-MALS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3240 Å2
ΔGint-30 kcal/mol
Surface area16770 Å2
Unit cell
Length a, b, c (Å)94.992, 94.992, 159.095
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

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Components

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Protein , 1 types, 1 molecules A

#1: Protein tRNA-specific 2-thiouridylase MnmA


Mass: 41882.969 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae TIGR4 (bacteria)
Gene: mnmA, trmU, SP_0118 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q97T38, tRNA-uridine 2-sulfurtransferase

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Non-polymers , 7 types, 294 molecules

#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PG6 / 1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE


Mass: 266.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O6
#6: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#7: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 282 / Source method: isolated from a natural source / Formula: H2O

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Details

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

Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 2M ammonium sulfate, 5% w/v PEG 400, 0.1M MES pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.978 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 26, 2023
RadiationMonochromator: Si filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.9→19.912 Å / Num. obs: 44516 / % possible obs: 95.4 % / Redundancy: 20.42 % / CC1/2: 0.999 / Rmerge(I) obs: 0.1301 / Rpim(I) all: 0.0295 / Rrim(I) all: 0.1335 / Net I/σ(I): 17.48
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. measured obsNum. unique allNum. unique obsCC1/2CC1/2 anomalousRpim(I) allRrim(I) allAbsDiff over sigma anomalous% possible anomalous% possible ellipsoidal% possible ellipsoidal anomalous% possible spherical% possible spherical anomalousRedundancy anomalous% possible all
5.98-19.912190.045455.414230542305222622261-0.1390.01060.04660.74610010010010010010.71100
4.74-5.9820.440.051750.354548945489222622261-0.0270.01180.05310.70499.910099.910099.911.08100
4.128-4.7421.320.05152.14743247432222522251-0.1360.01130.05230.66610010010010010011.41100
3.747-4.12821.160.064143.254709347093222622260.999-0.1040.01430.06570.71610010010010010011.23100
3.473-3.74719.850.081733.724419044190222622260.999-0.0860.01880.08380.74110010010010010010.49100
3.263-3.47319.460.109525.884330843308222622260.998-0.120.02540.11240.74899.910099.910099.910.26100
3.097-3.26320.590.153719.494583745837222622260.997-0.0740.03460.15760.75610010010010010010.82100
2.961-3.09720.980.211414.954668946689222522250.996-0.010.04710.21660.74610010010010010011100
2.845-2.9621.210.29611.084722047220222622260.992-0.0170.06570.30330.72510010010010010011.09100
2.745-2.84521.340.39658.454749847498222622260.9850.0210.08770.40620.72710010010010010011.15100
2.657-2.74521.490.49796.874783847838222622260.983-0.0310.10960.50990.71610010010010010011.22100
2.58-2.65721.550.67415.184797047970222622260.967-0.0210.14820.69040.72299.999.999.999.999.911.2399.9
2.512-2.5819.910.78294.294430844308222522250.944-0.0260.17920.80330.710010010010010010.35100
2.449-2.51120.590.89663.854584045840222622260.939-0.0340.20180.91930.70110010010010010010.71100
2.393-2.44919.331.07053.144302543025222622260.942-0.0190.2491.09930.72199.799.799.799.799.710.0299.7
2.337-2.39320.161.26572.724488644886222622260.882-0.0520.28781.29840.6993.593.393.593.393.510.4593.3
2.28-2.33720.561.41212.524576045760222622260.850.0260.31821.44790.73580.981.280.981.280.910.6881.2
2.21-2.2820.51.4552.464560345603222522250.8180.0240.32811.4920.71584.684.484.659.859.410.6684.4
2.122-2.2119.831.5692.234415244152222622260.768-0.0480.36021.61050.6829090.19041.440.210.490.1
1.902-2.12219.082.10111.664247742477222622260.574-0.0050.49172.15890.71673.273.373.212.311.310.273.3

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Processing

Software
NameVersionClassification
autoPROC1.0.5data processing
XDSJun 30, 2024data reduction
STARANISO2.4.16data scaling
PHENIX1.21.2_5419refinement
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→19.91 Å / SU ML: 0.1663 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.7313
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1976 2243 5.04 %
Rwork0.171 42270 -
obs0.1724 44513 67.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.34 Å2
Refinement stepCycle: LAST / Resolution: 1.9→19.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2830 0 115 282 3227
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00623014
X-RAY DIFFRACTIONf_angle_d0.86794059
X-RAY DIFFRACTIONf_chiral_restr0.0488421
X-RAY DIFFRACTIONf_plane_restr0.0072516
X-RAY DIFFRACTIONf_dihedral_angle_d21.26631140
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.940.399850.32464X-RAY DIFFRACTION1.72
1.94-1.990.4296150.3424248X-RAY DIFFRACTION6.49
1.99-2.040.4099260.2977465X-RAY DIFFRACTION12.15
2.04-2.090.3007390.2714808X-RAY DIFFRACTION20.93
2.09-2.160.3237560.25191290X-RAY DIFFRACTION32.71
2.16-2.220.29821040.24431790X-RAY DIFFRACTION46.65
2.22-2.30.27821290.24512527X-RAY DIFFRACTION65.52
2.3-2.40.28072020.23813485X-RAY DIFFRACTION90.72
2.4-2.50.2452220.23743896X-RAY DIFFRACTION99.83
2.51-2.640.24471730.20353929X-RAY DIFFRACTION100
2.64-2.80.2122000.19413879X-RAY DIFFRACTION100
2.8-3.020.17931920.17273920X-RAY DIFFRACTION100
3.02-3.320.17272210.16523916X-RAY DIFFRACTION100
3.32-3.80.16981950.14033971X-RAY DIFFRACTION100
3.8-4.770.15382060.12553994X-RAY DIFFRACTION100
4.78-19.910.20082580.16814088X-RAY DIFFRACTION99.95
Refinement TLS params.Method: refined / Origin x: 6.35604507787 Å / Origin y: -38.5380451591 Å / Origin z: -22.6701608298 Å
111213212223313233
T0.184778591146 Å2-0.0350598918044 Å20.037970956157 Å2-0.240084449579 Å2-0.0321326652629 Å2--0.241415922718 Å2
L1.53663993998 °20.209559754913 °21.05154475071 °2-0.743995980078 °2-0.0158317023684 °2--2.83280486525 °2
S0.187469457182 Å °0.108955028402 Å °-0.057887115876 Å °0.225979324598 Å °-0.107332893344 Å °0.126196496848 Å °0.103553135729 Å °-0.297787243842 Å °-0.0858724210926 Å °
Refinement TLS groupSelection details: all

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