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- PDB-7sex: M. tb EgtD in complex with TGX221 -

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Basic information

Entry
Database: PDB / ID: 7sex
TitleM. tb EgtD in complex with TGX221
ComponentsHistidine N-alpha-methyltransferase
KeywordsTRANSFERASE / Ergothioneine biosynthesis pathway / Rossmann fold domain / histidine/histamine derivatives / SAM dependent methyltransferase
Function / homology
Function and homology information


ergothioneine biosynthetic process / L-histidine Nalpha-methyltransferase / dimethylhistidine N-methyltransferase activity / aminoacyl-tRNA ligase activity / protein methyltransferase activity / methylation
Similarity search - Function
Methyltransferase EgtD-like / Histidine-specific methyltransferase, SAM-dependent / Histidine N-alpha-methyltransferase, Actinobacteria-type / Histidine N-alpha-methyltransferase / Histidine-specific methyltransferase, SAM-dependent / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
Chem-93I / Histidine N-alpha-methyltransferase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsSudasinghe, T.D. / Ronning, D.R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Sci Rep / Year: 2021
Title: Inhibitors of Mycobacterium tuberculosis EgtD target both substrate binding sites to limit hercynine production.
Authors: Sudasinghe, T.D. / Banco, M.T. / Ronning, D.R.
History
DepositionOct 2, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 1, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: 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: Histidine N-alpha-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8634
Polymers35,3151
Non-polymers5493
Water90150
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.019, 69.019, 140.922
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-543-

HOH

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Components

#1: Protein Histidine N-alpha-methyltransferase / Histidine trimethyltransferase


Mass: 35314.789 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: egtD / Production host: Escherichia coli (E. coli)
References: UniProt: A0A045KE74, L-histidine Nalpha-methyltransferase
#2: Chemical ChemComp-93I / 7-methyl-2-morpholin-4-yl-9-[(1~{R})-1-phenylazanylethyl]-3~{H}-pyrido[1,2-a]pyrimidin-4-one


Mass: 364.441 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H24N4O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 50 / 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: 2.38 Å3/Da / Density % sol: 48.24 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, hanging drop
Details: 0.2 M potassium phosphate dibasic and 20 % w/v polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.98 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 31, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.2→49.31 Å / Num. obs: 17958 / % possible obs: 99.78 % / Redundancy: 1 % / Biso Wilson estimate: 38.47 Å2 / CC1/2: 0.95 / Rmerge(I) obs: 0.08 / Net I/σ(I): 10
Reflection shellResolution: 2.201→2.279 Å / Num. unique obs: 1712 / CC1/2: 0.67

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
SCALAdata scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4UY5

4uy5


Resolution: 2.2→49.31 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.4 / Phase error: 20.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2298 1796 10 %
Rwork0.1807 16161 -
obs0.1856 17957 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 103.35 Å2 / Biso mean: 42.9703 Å2 / Biso min: 23.46 Å2
Refinement stepCycle: final / Resolution: 2.2→49.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2487 0 39 50 2576
Biso mean--79.5 45.57 -
Num. residues----321
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2-2.260.23361300.17531176130698
2.26-2.330.2441370.181612231360100
2.33-2.40.27471350.194412161351100
2.4-2.490.24931360.193712231359100
2.49-2.590.28111350.201912161351100
2.59-2.70.25621360.195312271363100
2.71-2.850.27221370.196712261363100
2.85-3.030.2611380.190612441382100
3.03-3.260.22091370.190512391376100
3.26-3.590.20861390.175112521391100
3.59-4.110.23641400.172912621402100
4.11-5.170.20851430.160612771420100
5.17-49.310.20671530.187313801533100
Refinement TLS params.Method: refined / Origin x: -16.6702 Å / Origin y: 8.2787 Å / Origin z: 4.7753 Å
111213212223313233
T0.3363 Å2-0.0016 Å2-0.0345 Å2-0.2348 Å2-0.0446 Å2--0.2803 Å2
L2.6549 °20.2997 °20.4853 °2-0.8784 °2-0.41 °2--0.9703 °2
S-0.1304 Å °-0.102 Å °0.1949 Å °0.0612 Å °0.0494 Å °-0.0905 Å °-0.1091 Å °0.057 Å °0.0869 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 321
2X-RAY DIFFRACTION1allA401 - 404
3X-RAY DIFFRACTION1allS1 - 59

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