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- PDB-2gq2: Mycobacterium tuberculosis ThyX-NADP complex -

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Basic information

Entry
Database: PDB / ID: 2gq2
TitleMycobacterium tuberculosis ThyX-NADP complex
ComponentsThymidylate synthase thyX
KeywordsTRANSFERASE / M.TUBERCULOSIS / THYX / FDTS / TSCP / Flavin dependent Thymidylate synthase / inhibitor design / bivalent drugs
Function / homology
Function and homology information


thymidylate synthase (FAD) / thymidylate synthase (FAD) activity / thymidylate synthase activity / dTMP biosynthetic process / dTTP biosynthetic process / NADPH binding / flavin adenine dinucleotide binding / methylation
Similarity search - Function
Alpha-Beta Plaits - #3180 / Helix Hairpins - #440 / Helix Hairpins - #450 / Thymidylate synthase ThyX / Thymidylate synthase ThyX superfamily / Thymidylate synthase complementing protein / Flavin-dependent thymidylate synthase (thyX) domain profile. / Helix Hairpins / Helix non-globular / Special ...Alpha-Beta Plaits - #3180 / Helix Hairpins - #440 / Helix Hairpins - #450 / Thymidylate synthase ThyX / Thymidylate synthase ThyX superfamily / Thymidylate synthase complementing protein / Flavin-dependent thymidylate synthase (thyX) domain profile. / Helix Hairpins / Helix non-globular / Special / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
IODIDE ION / : / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / TRIETHYLENE GLYCOL / Flavin-dependent thymidylate synthase / Flavin-dependent thymidylate synthase
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsSampathkumar, P. / Turley, S. / Sibley, C.H. / Hol, W.G.
Citation
Journal: J.Mol.Biol. / Year: 2006
Title: NADP+ expels both the co-factor and a substrate analog from the Mycobacterium tuberculosis ThyX active site: opportunities for anti-bacterial drug design.
Authors: Sampathkumar, P. / Turley, S. / Sibley, C.H. / Hol, W.G.
#1: Journal: J.Mol.Biol. / Year: 2005
Title: Structure of the Mycobacterium tuberculosis Flavin Dependent Thymidylate Synthase (MtbThyX) at 2.0A Resolution
Authors: Sampathkumar, P. / Turley, S. / Ulmer, J.E. / Rhie, H.G. / Sibley, C.H. / Hol, W.G.
History
DepositionApr 19, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 27, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 30, 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.end_auth_comp_id
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.6Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Thymidylate synthase thyX
B: Thymidylate synthase thyX
C: Thymidylate synthase thyX
D: Thymidylate synthase thyX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,70835
Polymers115,8804
Non-polymers5,82831
Water6,900383
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25120 Å2
ΔGint-60 kcal/mol
Surface area34310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.007, 78.090, 88.514
Angle α, β, γ (deg.)90.00, 95.67, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51A
61B
71C
81D
91A
101B
111C
121D
131A
141B
151C
161D

NCS domain segments:

Ens-ID: 1 / Refine code: 4

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRSERSERAA4 - 484 - 48
21THRTHRSERSERBB4 - 484 - 48
31THRTHRSERSERCC4 - 484 - 48
41THRTHRSERSERDD4 - 484 - 48
52THRTHRTYRTYRAA56 - 10856 - 108
62THRTHRTYRTYRBB54 - 10854 - 108
72THRTHRTYRTYRCC54 - 10854 - 108
82THRTHRTYRTYRDD54 - 10854 - 108
93VALVALALAALAAA116 - 152116 - 152
103VALVALALAALABB116 - 152116 - 152
113VALVALALAALACC116 - 152116 - 152
123VALVALALAALADD116 - 152116 - 152
134LYSLYSSERSERAA165 - 244165 - 244
144LYSLYSSERSERBB165 - 244165 - 244
154LYSLYSSERSERCC165 - 244165 - 244
164LYSLYSSERSERDD165 - 244165 - 244
DetailsBiological assembly is a tetramer composed of A, B, C and D chains

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Thymidylate synthase thyX / TS / TSase


Mass: 28969.977 Da / Num. of mol.: 4 / Mutation: I65M / L175M double mutant
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Species: Mycobacterium tuberculosis / Strain: H37RV / Gene: thyX, RV2754C / Plasmid: pET24d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS
References: UniProt: P66930, UniProt: P9WG57*PLUS, thymidylate synthase (FAD)

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Non-polymers , 6 types, 414 molecules

#2: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: I
#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#4: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 383 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.17 Å3/Da / Density % sol: 43.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 100mM sodium acetate, 200mM pottasium iodide, 2mM DTT and 13-15% PEG3350, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 18, 2004
RadiationMonochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 64080 / % possible obs: 97 % / Redundancy: 2.4 % / Biso Wilson estimate: 23.4 Å2 / Rsym value: 0.072 / Net I/σ(I): 10
Reflection shellResolution: 2→2.07 Å / Mean I/σ(I) obs: 3.3 / Num. unique all: 6498 / Rsym value: 0.369 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
ADSCdata collection
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2AF6

2af6


Resolution: 2.1→35.2 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.906 / SU B: 5.21 / SU ML: 0.143 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.266 / ESU R Free: 0.209
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
RfactorNum. reflection% reflectionSelection details
Rfree0.25464 2809 5 %RANDOM
Rwork0.21185 ---
obs0.21404 53189 96.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 25.97 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.209 Å0.266 Å
Luzzati sigma a-0.143 Å
Refinement stepCycle: LAST / Resolution: 2.1→35.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6983 0 263 383 7629
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0227411
X-RAY DIFFRACTIONr_angle_refined_deg1.3991.97510140
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8835914
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.38822.395309
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.737151047
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2881563
X-RAY DIFFRACTIONr_chiral_restr0.0870.21172
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025574
X-RAY DIFFRACTIONr_nbd_refined0.2270.23445
X-RAY DIFFRACTIONr_nbtor_refined0.2950.25140
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1780.2440
X-RAY DIFFRACTIONr_metal_ion_refined0.1460.28
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.230.250
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.20.216
X-RAY DIFFRACTIONr_mcbond_it0.7061.54606
X-RAY DIFFRACTIONr_mcangle_it1.31827376
X-RAY DIFFRACTIONr_scbond_it2.05632837
X-RAY DIFFRACTIONr_scangle_it3.3234.52760
Refine LS restraints NCS

Ens-ID: 1 / Number: 1563 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Amedium positional0.380.5
2Bmedium positional0.370.5
3Cmedium positional0.460.5
4Dmedium positional0.380.5
1Amedium thermal0.862
2Bmedium thermal0.792
3Cmedium thermal0.872
4Dmedium thermal0.62
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.268 224 -
Rwork0.217 3967 -
obs--99.03 %

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