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- PDB-7sey: M. tb EgtD in complex with SGH -

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Basic information

Entry
Database: PDB / ID: 7sey
TitleM. tb EgtD in complex with SGH
ComponentsHistidine N-alpha-methyltransferase
KeywordsTRANSFERASE / Ergothioneine biosynthesis pathway / Rossmann fold domain / bi-substrate analogs / SAM dependent methyltransferase
Function / homology
Function and homology information


ergothioneine biosynthetic process / L-histidine Nalpha-methyltransferase / L-histidine N(alpha)-methyltransferase 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-92W / Histidine N-alpha-methyltransferase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.39 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)35,6912
Polymers35,3151
Non-polymers3761
Water1267
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.281, 69.281, 142.127
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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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-92W / 2-amino-1-[(3S)-3-methyl-4-(4-methylisoquinoline-5-sulfonyl)-1,4-diazepan-1-yl]ethan-1-one


Mass: 376.473 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H24N4O3S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 2.41 Å3/Da / Density % sol: 49.06 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, hanging drop
Details: 0.2 M succinic acid pH 7.0 and 20 % w/v polyethylene glycol 1,000

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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: 2.39→46.31 Å / Num. obs: 12689 / % possible obs: 88.1 % / Redundancy: 16.9 % / Biso Wilson estimate: 50.82 Å2 / CC1/2: 0.99 / Net I/σ(I): 10
Reflection shellResolution: 2.39→2.476 Å / Rmerge(I) obs: 1.925 / Num. unique obs: 759 / CC1/2: 0.634

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Processing

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

4uy5


Resolution: 2.39→46.31 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 36.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2821 2303 10.01 %
Rwork0.2197 20715 -
obs0.2259 23018 88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 100.95 Å2 / Biso mean: 56.2407 Å2 / Biso min: 41.33 Å2
Refinement stepCycle: final / Resolution: 2.39→46.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2487 0 26 7 2520
Biso mean--70.83 56.85 -
Num. residues----321
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.39-2.440.4862810.396675984052
2.44-2.50.4093990.36884093957
2.5-2.560.40011080.3504937104564
2.56-2.630.33821110.33261046115771
2.63-2.710.3721310.29891154128580
2.71-2.80.36331460.29761321146788
2.8-2.90.34281650.27051458162399
2.9-3.010.31951650.254214531618100
3.01-3.150.30341630.242114931656100
3.15-3.310.30761590.24491442160199
3.31-3.520.25741650.222214561621100
3.52-3.790.27271710.208414691640100
3.79-4.170.30481590.192814531612100
4.18-4.780.2741650.183614811646100
4.78-6.020.24441560.208914801636100
6.02-46.310.21331590.17511473163299
Refinement TLS params.Method: refined / Origin x: -17.1914 Å / Origin y: 8.0421 Å / Origin z: 4.8614 Å
111213212223313233
T0.3788 Å2-0.0078 Å2-0.0196 Å2-0.3004 Å2-0.0161 Å2--0.3564 Å2
L1.0802 °20.2022 °20.168 °2-0.1361 °2-0.2117 °2--0.5876 °2
S-0.0618 Å °0.0023 Å °0.0246 Å °0.0541 Å °0.0339 Å °-0.0064 Å °-0.0518 Å °-0.0231 Å °-0 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 321
2X-RAY DIFFRACTION1allA401
3X-RAY DIFFRACTION1allS1 - 11

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