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- PDB-4o7u: Etherocomplex of Enteroccocus faecalis thymidylate synthase with ... -

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Basic information

Entry
Database: PDB / ID: 4o7u
TitleEtherocomplex of Enteroccocus faecalis thymidylate synthase with 5-hydroxymethilene-6-hydrofolic acid and the phtalimidic inhibitor SS7
ComponentsThymidylate synthase
Keywordstransferase/transferase inhibitor / transferase / folate binding / transferase-transferase inhibitor complex
Function / homology
Function and homology information


thymidylate synthase / thymidylate synthase activity / dTMP biosynthetic process / dTTP biosynthetic process / methylation / cytosol
Similarity search - Function
Thymidylate Synthase; Chain A / Thymidylate synthase/dCMP hydroxymethylase domain / Thymidylate synthase, active site / Thymidylate synthase active site. / Thymidylate synthase / Thymidylate synthase/dCMP hydroxymethylase / Thymidylate synthase/dCMP hydroxymethylase domain / Thymidylate synthase/dCMP hydroxymethylase superfamily / Thymidylate synthase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-SS7 / 5-HYDROXYMETHYLENE-6-HYDROFOLIC ACID / Thymidylate synthase
Similarity search - Component
Biological speciesEnterococcus faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsMangani, S. / Pozzi, C.
CitationJournal: Eur.J.Med.Chem. / Year: 2016
Title: X-ray crystal structures of Enterococcus faecalis thymidylate synthase with folate binding site inhibitors.
Authors: Catalano, A. / Luciani, R. / Carocci, A. / Cortesi, D. / Pozzi, C. / Borsari, C. / Ferrari, S. / Mangani, S.
History
DepositionDec 26, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 31, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 5, 2016Group: Database references
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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)146,89312
Polymers145,5444
Non-polymers1,3498
Water3,693205
1
A: Thymidylate synthase
B: Thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,4385
Polymers72,7722
Non-polymers6663
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6140 Å2
ΔGint-54 kcal/mol
Surface area25610 Å2
MethodPISA
2
C: Thymidylate synthase
D: Thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,4567
Polymers72,7722
Non-polymers6845
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5570 Å2
ΔGint-49 kcal/mol
Surface area24470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.082, 94.225, 96.816
Angle α, β, γ (deg.)90.00, 94.33, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Thymidylate synthase / TS / TSase


Mass: 36385.977 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis (bacteria) / Strain: ATCC 700802 / V583 / Gene: thyA, EF_1576 / Production host: Escherichia coli (E. coli) / References: UniProt: Q834R3, thymidylate synthase

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Non-polymers , 5 types, 213 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-THF / 5-HYDROXYMETHYLENE-6-HYDROFOLIC ACID


Mass: 473.439 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H23N7O7
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-SS7 / 4-{[(2S)-2-(1,3-dioxo-1,3-dihydro-2H-isoindol-2-yl)propyl]oxy}-3,5-dimethylphenyl acetate


Mass: 367.395 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H21NO5
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 205 / 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: 2.25 Å3/Da / Density % sol: 45.39 %
Crystal growTemperature: 297 K / Method: microbatch under oil / pH: 7
Details: 6.5 mg/mL EfTS, 3.2 M ammonium sulfate, 0.1 M HEPES, co-cystallization with 4 mM SS7 in DMSO in 1/10 SS7/EfTS volume ratio, pH 7.0, microbatch under oil, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.936 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 5, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.936 Å / Relative weight: 1
ReflectionResolution: 2.4→67.43 Å / Num. all: 38554 / Num. obs: 38554 / % possible obs: 76.5 % / Observed criterion σ(F): 1.4 / Observed criterion σ(I): 2 / Redundancy: 2.4 % / Rmerge(I) obs: 0.124 / Net I/σ(I): 6.5
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.354 / Mean I/σ(I) obs: 3.2 / % possible all: 75.5

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Processing

Software
NameVersionClassification
DNAdata collection
MOLREPphasing
REFMAC5.7.0029refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→55.67 Å / Cor.coef. Fo:Fc: 0.906 / Cor.coef. Fo:Fc free: 0.83 / SU B: 10.366 / SU ML: 0.241 / Cross valid method: THROUGHOUT / ESU R Free: 0.402 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.28671 1962 5.1 %RANDOM
Rwork0.21187 ---
obs0.21561 36573 76.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.199 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å2-0.01 Å2
2--0 Å20 Å2
3----0.02 Å2
Refine analyze
FreeObs
Luzzati sigma a0.405 Å0.225 Å
Refinement stepCycle: LAST / Resolution: 2.4→55.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9738 0 89 205 10032
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01910096
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3011.95313685
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.14751185
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.36724.291522
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.855151669
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.161550
X-RAY DIFFRACTIONr_chiral_restr0.0930.21425
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0217844
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.611.4914764
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.082.235941
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.5731.5595332
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.359 132 -
Rwork0.254 2673 -
obs--75.12 %

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