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- PDB-9i7r: Crystal structure of MnmA D100C mutant from Streptococcus pneumon... -

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Basic information

Entry
Database: PDB / ID: 9i7r
TitleCrystal structure of MnmA D100C mutant from Streptococcus pneumoniae with [4Fe-5Se] cluster
ComponentstRNA-specific 2-thiouridylase MnmA
KeywordsTRANSFERASE / iron-sulfur cluster / tRNA thiolation / sulfur / selenium / thiouridylase
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
FORMIC ACID / SELENIUM ATOM / Fe4-Se4 cluster / tRNA-specific 2-thiouridylase MnmA
Similarity search - Component
Biological speciesStreptococcus pneumoniae TIGR4 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.37 Å
AuthorsGervason, S. / Golinelli-Pimpaneau, B.
Funding support France, 2items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-22-CE44-0012 France
Agence Nationale de la Recherche (ANR)ANR-11-labx-0011 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
DepositionFeb 1, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 19, 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)44,26530
Polymers41,8711
Non-polymers2,39429
Water3,801211
1
A: tRNA-specific 2-thiouridylase MnmA
hetero molecules

A: tRNA-specific 2-thiouridylase MnmA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,53160
Polymers83,7422
Non-polymers4,78958
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area13030 Å2
ΔGint-159 kcal/mol
Surface area28220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.272, 94.272, 158.986
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
Components on special symmetry positions
IDModelComponents
11A-420-

SE

21A-708-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein tRNA-specific 2-thiouridylase MnmA


Mass: 41871.023 Da / Num. of mol.: 1 / Mutation: D100C
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 , 5 types, 240 molecules

#2: Chemical ChemComp-SFS / Fe4-Se4 cluster


Mass: 539.220 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4Se4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: CH2O2 / Feature type: SUBJECT OF INVESTIGATION
#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 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-SE / SELENIUM ATOM


Mass: 78.960 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Se / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 211 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 4.87 Å3/Da / Density % sol: 74.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: ANAEROBY (<1.5 ppm O2) 3.5M Sodium formate 0.1M Tris pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.97487 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 23, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97487 Å / Relative weight: 1
ReflectionResolution: 2.37→19.85 Å / Num. obs: 27317 / % possible obs: 80.7 % / Redundancy: 30.8 % / Biso Wilson estimate: 39.82 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.257 / Rpim(I) all: 0.047 / Rrim(I) all: 0.261 / Net I/σ(I): 12.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
7.018-19.850.09233.62113660.9990.0170.093
5.561-7.0170.14723.73513660.99730.0270.149
4.845-5.5610.14223.46613660.99750.0270.145
4.399-4.8450.12924.54713650.99750.0250.131
4.076-4.3990.14923.32613660.99740.0270.151
3.834-4.0760.18719.40313660.99550.0340.19
3.636-3.8340.22117.1713660.99450.040.225
3.476-3.6360.25315.60813660.99380.0450.257
3.341-3.4750.30712.96313660.99230.0550.312
3.224-3.3410.36211.00713650.99070.0650.368
3.12-3.2240.4648.75313660.98420.0830.472
3.029-3.120.5577.16113660.9820.0990.566
2.947-3.0290.6635.92813660.97390.1180.673
2.875-2.9470.824.68413660.97130.1450.833
2.809-2.8751.0653.65113660.94930.1931.082
2.748-2.8091.3092.82413660.92010.2471.332
2.691-2.7481.6972.28713650.87860.3121.726
2.639-2.6912.0921.80613660.88460.382.127
2.58-2.6392.4881.48613660.82360.4712.533
2.37-2.582.3211.55613660.84280.4362.362

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
autoPROC1.0.5data processing
XDSJun 30, 2023data reduction
STARANISO2.4.16data scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.37→19.85 Å / SU ML: 0.2265 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.3083
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1986 1364 4.99 %
Rwork0.1686 25948 -
obs0.1701 27312 80.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.59 Å2
Refinement stepCycle: LAST / Resolution: 2.37→19.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2854 0 75 211 3140
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00762971
X-RAY DIFFRACTIONf_angle_d0.91743993
X-RAY DIFFRACTIONf_chiral_restr0.0482417
X-RAY DIFFRACTIONf_plane_restr0.0069518
X-RAY DIFFRACTIONf_dihedral_angle_d19.4721081
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.37-2.450.446380.3597137X-RAY DIFFRACTION4.41
2.45-2.550.3155400.3034736X-RAY DIFFRACTION23.09
2.55-2.670.2911000.27962443X-RAY DIFFRACTION76.67
2.67-2.810.29511620.23833184X-RAY DIFFRACTION99.73
2.81-2.980.26531610.2333191X-RAY DIFFRACTION99.97
2.98-3.210.19991770.18563192X-RAY DIFFRACTION100
3.21-3.530.20071590.16743214X-RAY DIFFRACTION100
3.53-4.040.18531880.13313217X-RAY DIFFRACTION100
4.04-5.080.15631590.12023270X-RAY DIFFRACTION100
5.08-19.850.17722100.16713364X-RAY DIFFRACTION99.89
Refinement TLS params.Method: refined / Origin x: 29.942 Å / Origin y: 24.748 Å / Origin z: 3.091 Å
111213212223313233
T0.214509363271 Å20.0264753111638 Å20.0065544646707 Å2-0.234361601794 Å20.0363361842958 Å2--0.270552807282 Å2
L0.817043712971 °2-0.388310314122 °2-0.514586683079 °2-1.14852259629 °21.30307145342 °2--3.31906265134 °2
S0.0672410280456 Å °-0.143415084116 Å °-0.066222995204 Å °-0.0973294612047 Å °0.00468515357755 Å °-0.094633488898 Å °0.147624223954 Å °0.212803640071 Å °-0.0886735230696 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND ( RESID 3:373 OR RESID 401:416 OR RESID 501:711 OR RESID 417:429 ) )A3 - 373
2X-RAY DIFFRACTION1( CHAIN A AND ( RESID 3:373 OR RESID 401:416 OR RESID 501:711 OR RESID 417:429 ) )A401 - 416
3X-RAY DIFFRACTION1( CHAIN A AND ( RESID 3:373 OR RESID 401:416 OR RESID 501:711 OR RESID 417:429 ) )A501 - 711
4X-RAY DIFFRACTION1( CHAIN A AND ( RESID 3:373 OR RESID 401:416 OR RESID 501:711 OR RESID 417:429 ) )A417 - 429

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