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- PDB-7sf5: M. tb EgtD in complex with HD3 -

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Basic information

Entry
Database: PDB / ID: 7sf5
TitleM. tb EgtD in complex with HD3
ComponentsHistidine N-alpha-methyltransferase
KeywordsTRANSFERASE / SAM dependent methyl transferase / peptide like inhibitor / SAM binding domain / Histidine binding domain
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
N-(benzylcarbamothioyl)-L-histidine / Histidine N-alpha-methyltransferase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.52 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 3, 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 ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)71,2384
Polymers70,6302
Non-polymers6092
Water1,36976
1
A: Histidine N-alpha-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6192
Polymers35,3151
Non-polymers3041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Histidine N-alpha-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6192
Polymers35,3151
Non-polymers3041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.146, 70.277, 143.883
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: LYS / End label comp-ID: LYS / Auth seq-ID: 1 - 321 / Label seq-ID: 1 - 321

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain AAA
2chain BBB

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Components

#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 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A045KE74, L-histidine Nalpha-methyltransferase
#2: Chemical ChemComp-95I / N-(benzylcarbamothioyl)-L-histidine


Mass: 304.367 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H16N4O2S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / 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: 2.47 Å3/Da / Density % sol: 50.3 %
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: Aug 31, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.52→50.27 Å / Num. obs: 24381 / % possible obs: 99.86 % / Redundancy: 1 % / CC1/2: 0.98 / Net I/σ(I): 11
Reflection shellResolution: 2.52→2.61 Å / Num. unique obs: 2384 / CC1/2: 0.55

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
SCALAdata scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4UY5

4uy5


Resolution: 2.52→50.27 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2676 1994 8.18 %
Rwork0.1977 22380 -
obs0.2033 24374 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 86.43 Å2 / Biso mean: 35.6355 Å2 / Biso min: 10.75 Å2
Refinement stepCycle: final / Resolution: 2.52→50.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4968 0 42 76 5086
Biso mean--51.24 34.36 -
Num. residues----642
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1992X-RAY DIFFRACTION6.339TORSIONAL
12B1992X-RAY DIFFRACTION6.339TORSIONAL
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 (%)
2.52-2.580.34251340.29771553168799
2.58-2.650.33741440.260315691713100
2.65-2.730.2911450.246315521697100
2.73-2.820.31731370.23416061743100
2.82-2.920.34341380.231815641702100
2.92-3.040.28221360.228215771713100
3.04-3.170.32041430.218215981741100
3.17-3.340.29541410.197115811722100
3.34-3.550.24551410.193215941735100
3.55-3.820.26131450.186615891734100
3.82-4.210.27971370.174316211758100
4.21-4.820.23471460.152516081754100
4.82-6.070.2451480.196916451793100
6.07-50.270.191590.170217231882100

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