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- PDB-7scf: M. tb EgtD in complex with HD2 -

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Basic information

Entry
Database: PDB / ID: 7scf
TitleM. tb EgtD in complex with HD2
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 / : / 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-8YI / DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / Histidine N-alpha-methyltransferase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.67 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
DepositionSep 28, 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
B: Histidine N-alpha-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,48918
Polymers70,6302
Non-polymers1,86016
Water1,60389
1
A: Histidine N-alpha-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,45011
Polymers35,3151
Non-polymers1,13510
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Histidine N-alpha-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0397
Polymers35,3151
Non-polymers7256
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.102, 71.570, 145.095
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 35314.789 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria)
Gene: egtD, C0094_20235, DSI38_25660, E5M05_18135, E5M52_16355, E5M78_15990, ERS007657_01802, ERS007663_00740, ERS007665_01629, ERS007670_03296, ERS007741_03430, ERS013471_00673, ERS024276_01805, ...Gene: egtD, C0094_20235, DSI38_25660, E5M05_18135, E5M52_16355, E5M78_15990, ERS007657_01802, ERS007663_00740, ERS007665_01629, ERS007670_03296, ERS007741_03430, ERS013471_00673, ERS024276_01805, ERS094182_02516, F6W99_02380, GCL30_14140, SAMEA2683035_00801
Production host: Escherichia coli (E. coli)
References: UniProt: A0A045KE74, L-histidine Nalpha-methyltransferase

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Non-polymers , 5 types, 105 molecules

#2: Chemical ChemComp-8YI / (2S)-3-(1H-imidazol-5-yl)-2-(1H-pyrrol-1-yl)propanoic acid


Mass: 205.213 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H11N3O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.54 Å3/Da / Density % sol: 51.57 %
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: 2.67→50.95 Å / Num. obs: 21089 / % possible obs: 99.84 % / Redundancy: 1 % / CC1/2: 0.96 / Rmerge(I) obs: 0.1 / Net I/σ(I): 10.89
Reflection shellResolution: 2.67→2.67 Å / Rmerge(I) obs: 0.45 / Num. unique obs: 2068 / CC1/2: 0.44

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.27data extraction
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4UY5

4uy5


Resolution: 2.67→50.95 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2801 1996 9.47 %
Rwork0.2128 19079 -
obs0.2193 21075 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 47.56 Å2 / Biso mean: 29.4438 Å2 / Biso min: 21.03 Å2
Refinement stepCycle: final / Resolution: 2.67→50.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4974 0 99 89 5162
Biso mean--31.58 28.29 -
Num. residues----642
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.67-2.730.33381330.27771279141296
2.74-2.810.38151420.283213261468100
2.81-2.890.32661390.273913641503100
2.89-2.980.31531410.266513541495100
2.98-3.090.31511450.256513331478100
3.09-3.220.31021440.237113321476100
3.22-3.360.31351400.224613641504100
3.36-3.540.28861370.206113631500100
3.54-3.760.24951410.196913601501100
3.76-4.050.27361470.195213601507100
4.05-4.460.25161430.173913771520100
4.46-5.10.23991420.176413781520100
5.1-6.420.31691460.225914011547100
6.43-50.950.20681560.177514881644100
Refinement TLS params.Method: refined / Origin x: -22.245 Å / Origin y: -5.5358 Å / Origin z: 18.0802 Å
111213212223313233
T0.214 Å2-0.0369 Å2-0.0061 Å2-0.2053 Å20.0004 Å2--0.2127 Å2
L0.2177 °2-0.155 °20.0191 °2-0.1777 °2-0.0541 °2--0.1615 °2
S0.0019 Å °-0.0269 Å °0.031 Å °-0.0101 Å °0.0013 Å °-0.0229 Å °-0.0655 Å °0.0596 Å °-0.0022 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 321
2X-RAY DIFFRACTION1allA401 - 501
3X-RAY DIFFRACTION1allB1 - 401
4X-RAY DIFFRACTION1allB402 - 501
5X-RAY DIFFRACTION1allD1 - 2
6X-RAY DIFFRACTION1allS1 - 114

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