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- PDB-7sf4: M. tb EgtD in complex with imatinib -

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Basic information

Entry
Database: PDB / ID: 7sf4
TitleM. tb EgtD in complex with imatinib
ComponentsHistidine N-alpha-methyltransferase
KeywordsTRANSFERASE / Ergothioneine biosynthesis pathway / Rossmann fold domain / histidine binding site / 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
2-AMINO-4-PYRIDYL-PYRIMIDINE / 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 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)72,02318
Polymers70,6302
Non-polymers1,39316
Water3,207178
1
A: Histidine N-alpha-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,22812
Polymers35,3151
Non-polymers91311
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Histidine N-alpha-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7956
Polymers35,3151
Non-polymers4815
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.980, 71.131, 144.557
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
11(chain A and (resid 1 through 321 or resid 401 through 403 or resid 405 through 406))
21(chain B and (resid 1 through 321 or resid 401 through 402 or resid 404 through 405))

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYLYSLYS(chain A and (resid 1 through 321 or resid 401 through 403 or resid 405 through 406))AA1 - 3211 - 321
12XDKXDKGOLGOL(chain A and (resid 1 through 321 or resid 401 through 403 or resid 405 through 406))AC - E401 - 403
13EDOEDOEDOEDO(chain A and (resid 1 through 321 or resid 401 through 403 or resid 405 through 406))AG - H405 - 406
21GLYGLYLYSLYS(chain B and (resid 1 through 321 or resid 401 through 402 or resid 404 through 405))BB1 - 3211 - 321
22XDKXDKGOLGOL(chain B and (resid 1 through 321 or resid 401 through 402 or resid 404 through 405))BN - O401 - 402
23GOLGOLEDOEDO(chain B and (resid 1 through 321 or resid 401 through 402 or resid 404 through 405))BQ - R404 - 405

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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-XDK / 2-AMINO-4-PYRIDYL-PYRIMIDINE


Mass: 172.187 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H8N4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 178 / 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: 2.51 Å3/Da / Density % sol: 51.01 %
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: 2.39→50.7 Å / Num. obs: 28869 / % possible obs: 96.77 % / Redundancy: 1 % / Biso Wilson estimate: 29.82 Å2 / CC1/2: 0.95 / Net I/σ(I): 10
Reflection shellResolution: 2.39→2.45 Å / Num. unique obs: 690 / CC1/2: 0.952

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Processing

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

4uy5


Resolution: 2.39→50.7 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 27.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2636 2002 6.93 %
Rwork0.2207 26867 -
obs0.2237 28869 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 64.15 Å2 / Biso mean: 34.3192 Å2 / Biso min: 22.95 Å2
Refinement stepCycle: final / Resolution: 2.39→50.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4974 0 94 178 5246
Biso mean--40.66 34.7 -
Num. residues----642
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1995X-RAY DIFFRACTION6.283TORSIONAL
12B1995X-RAY DIFFRACTION6.283TORSIONAL
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 (%)
2.39-2.450.35691390.32161871201099
2.45-2.520.36171360.296718842020100
2.52-2.590.31351450.283318912036100
2.59-2.670.35071400.276918902030100
2.67-2.770.32291390.267718922031100
2.77-2.880.31311400.254919142054100
2.88-3.010.27531430.24218792022100
3.01-3.170.30021410.230119232064100
3.17-3.370.31451480.213718972045100
3.37-3.630.23681420.200419322074100
3.63-3.990.24121420.193519212063100
3.99-4.570.21191450.173119412086100
4.57-5.760.22111430.201719792122100
5.76-50.70.21141590.19742053221299
Refinement TLS params.Method: refined / Origin x: 12.1218 Å / Origin y: 40.8504 Å / Origin z: -18.1202 Å
111213212223313233
T0.2238 Å20.028 Å20.0103 Å2-0.2598 Å2-0.0126 Å2--0.2176 Å2
L0.2054 °20.0454 °20.0054 °2-0.187 °2-0.0388 °2--0.0977 °2
S-0.0044 Å °0.0486 Å °-0.04 Å °0.0094 Å °0.0136 Å °-0.0318 Å °0.0452 Å °0.0675 Å °-0.0127 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 321
2X-RAY DIFFRACTION1allA401 - 411
3X-RAY DIFFRACTION1allB1 - 321
4X-RAY DIFFRACTION1allB401 - 405
5X-RAY DIFFRACTION1allS405 - 649
6X-RAY DIFFRACTION1allC1 - 3

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