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- PDB-4fqs: Crystal Structure of Mycobacterium tuberculosis ThyA in complex w... -

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Basic information

Entry
Database: PDB / ID: 4fqs
TitleCrystal Structure of Mycobacterium tuberculosis ThyA in complex with UMP and Pemetrexed
ComponentsThymidylate synthase
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / Transferase / Folate binding / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


dUMP catabolic process / thymidylate synthase / thymidylate synthase activity / dTMP biosynthetic process / dTTP biosynthetic process / methylation / response to antibiotic / cytoplasm / cytosol
Similarity search - Function
Thymidylate Synthase; Chain A / Thymidylate synthase/dCMP hydroxymethylase domain / Thymidylate synthase/dCMP hydroxymethylase / Thymidylate synthase, active site / Thymidylate synthase active site. / Thymidylate synthase / Thymidylate synthase/dCMP hydroxymethylase domain / Thymidylate synthase/dCMP hydroxymethylase superfamily / Thymidylate synthase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-LYA / 2'-DEOXYURIDINE 5'-MONOPHOSPHATE / Thymidylate synthase / Thymidylate synthase ThyA
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsReddy, M.C.M. / Bruning, J.B. / Harshbarger, W. / Sacchettini, J.C.
CitationJournal: To be Published
Title: Crystal structure of binary and ternary complexes of thymidylate synthase (ThyA) from Mycobacterium tuberculosis: insights into the selectivity and mode of inhibition
Authors: Reddy, M.C.M. / Bruning, J.B. / Harshbarger, W. / Sacchettini, J.C.
History
DepositionJun 25, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thymidylate synthase
B: Thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,2416
Polymers59,7702
Non-polymers1,4714
Water18,5911032
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4190 Å2
ΔGint-14 kcal/mol
Surface area19920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.099, 57.045, 113.694
Angle α, β, γ (deg.)90.000, 107.950, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-419-

HOH

21B-442-

HOH

31B-498-

HOH

41B-535-

HOH

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Components

#1: Protein Thymidylate synthase / TS / TSase


Mass: 29884.830 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: MT2834, MTV002.29c, Rv2764c, thyA / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P67044, UniProt: P9WFR9*PLUS, thymidylate synthase
#2: Chemical ChemComp-UMP / 2'-DEOXYURIDINE 5'-MONOPHOSPHATE / DUMP


Mass: 308.182 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H13N2O8P
#3: Chemical ChemComp-LYA / 2-{4-[2-(2-AMINO-4-OXO-4,7-DIHYDRO-3H-PYRROLO[2,3-D]PYRIMIDIN-5-YL)-ETHYL]-BENZOYLAMINO}-PENTANEDIOIC ACID / LY231514


Mass: 427.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H21N5O6 / Comment: medication, chemotherapy*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1032 / Source method: isolated from a natural source / Formula: H2O

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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: 2.58 Å3/Da / Density % sol: 52.39 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Tris pH 7.0, 200 mM NaCl, and 30% polyethylene glycol 3K, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 5, 2010 / Details: mirrors
RadiationMonochromator: Mirrors / Protocol: Single / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 55678 / % possible obs: 75 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIX1.6.4_486refinement
PDB_EXTRACT3.11data extraction
CrystalCleardata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→21.878 Å / Occupancy max: 1 / Occupancy min: 0.29 / FOM work R set: 0.8642 / SU ML: 0.19 / σ(F): 1.34 / Phase error: 20.09 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.1989 2775 4.99 %
Rwork0.1553 --
obs0.1574 55636 97.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 55.206 Å2 / ksol: 0.326 e/Å3
Displacement parametersBiso max: 76.72 Å2 / Biso mean: 24.4237 Å2 / Biso min: 9.2 Å2
Baniso -1Baniso -2Baniso -3
1--0.2235 Å20 Å2-0.1496 Å2
2--4.4447 Å2-0 Å2
3----4.2211 Å2
Refinement stepCycle: LAST / Resolution: 1.8→21.878 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4207 0 102 1032 5341
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074513
X-RAY DIFFRACTIONf_angle_d1.1686181
X-RAY DIFFRACTIONf_chiral_restr0.078648
X-RAY DIFFRACTIONf_plane_restr0.007787
X-RAY DIFFRACTIONf_dihedral_angle_d14.0411671
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.83010.23781240.1932485260994
1.8301-1.86330.2521430.18492646278998
1.8633-1.89910.24041400.17822623276398
1.8991-1.93790.20061190.15772633275298
1.9379-1.980.19361250.15482654277997
1.98-2.0260.21961350.15792576271197
2.026-2.07660.2221420.16792617275998
2.0766-2.13270.22431270.15652661278898
2.1327-2.19540.21411380.15442608274697
2.1954-2.26620.19281340.15532613274798
2.2662-2.34710.22381430.15342627277099
2.3471-2.4410.20271340.1572690282499
2.441-2.55190.1731650.15382627279299
2.5519-2.68630.20851490.15412685283499
2.6863-2.85420.23051480.15752689283799
2.8542-3.07410.20731690.15232641281099
3.0741-3.38240.18171300.14952683281398
3.3824-3.86950.18951390.15162656279598
3.8695-4.86630.15491240.13492712283699
4.8663-21.88010.20151470.17182735288298

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