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- PDB-5j7w: Enterococcus faecalis thymidylate synthase complex with methotrexate -

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Basic information

Entry
Database: PDB / ID: 5j7w
TitleEnterococcus faecalis thymidylate synthase complex with methotrexate
ComponentsThymidylate synthase
KeywordsTRANSFERASE / Enterococcus faecalis / thymidylate synthase / methotrexate / complex
Function / homology
Function and homology information


thymidylate synthase / thymidylate synthase activity / dTMP biosynthetic process / dTTP biosynthetic process / methylation / cytoplasm
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
METHOTREXATE / Thymidylate synthase
Similarity search - Component
Biological speciesEnterococcus faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsMangani, S. / Pozzi, C.
Funding support Italy, 1items
OrganizationGrant numberCountry
MIUR-PRIN2009200925BPZ5_004 Italy
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
DepositionApr 7, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 28, 2016Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)146,83710
Polymers145,5444
Non-polymers1,2936
Water3,207178
1
A: Thymidylate synthase
D: Thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,4195
Polymers72,7722
Non-polymers6473
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6040 Å2
ΔGint-55 kcal/mol
Surface area24600 Å2
MethodPISA
2
B: Thymidylate synthase
C: Thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,4195
Polymers72,7722
Non-polymers6473
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6150 Å2
ΔGint-54 kcal/mol
Surface area24480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.227, 94.144, 96.293
Angle α, β, γ (deg.)90.000, 94.140, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Thymidylate synthase / / 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 BL21(DE3) (bacteria) / References: UniProt: Q834R3, thymidylate synthase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-MTX / METHOTREXATE / Methotrexate


Mass: 454.439 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H22N8O5 / Comment: chemotherapy*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 178 / 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: 2.24 Å3/Da / Density % sol: 45.18 %
Crystal growTemperature: 297 K / Method: microbatch / pH: 7
Details: co-crystallization microbatch under oil 1:1 paraffin/silicon oil precipitant solution: 3.2 M ammonium sulfate and 0.1 M HEPES 6.5 mg/mL EfTS, co-cystallization with 4 mM MTX in DMSO in 1/10 ...Details: co-crystallization microbatch under oil 1:1 paraffin/silicon oil precipitant solution: 3.2 M ammonium sulfate and 0.1 M HEPES 6.5 mg/mL EfTS, co-cystallization with 4 mM MTX in DMSO in 1/10 MTX/EfTS volume ratio.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.936 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 6, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.936 Å / Relative weight: 1
ReflectionResolution: 2.45→67.23 Å / Num. obs: 37276 / % possible obs: 79.1 % / Redundancy: 4.2 % / CC1/2: 0.969 / Rmerge(I) obs: 0.187 / Rpim(I) all: 0.099 / Rrim(I) all: 0.213 / Net I/σ(I): 6.6 / Num. measured all: 155393 / Scaling rejects: 29
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.45-2.5540.4941699242530.7020.2750.5693.680.4
8.83-67.234.80.11636737650.9910.0560.12910.873.7

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Processing

Software
NameVersionClassification
Aimless0.5.1data scaling
PDB_EXTRACT3.2data extraction
MOSFLMdata reduction
MOLREPphasing
PHENIX(1.10.1_2155)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→96.04 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.829 / SU B: 11.979 / SU ML: 0.262 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.41 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2727 1731 4.9 %RANDOM
Rwork0.2 ---
obs0.2035 33282 78.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 75.83 Å2 / Biso mean: 16.23 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0 Å20.08 Å2
2---0.05 Å2-0 Å2
3---0.05 Å2
Refinement stepCycle: final / Resolution: 2.5→96.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9607 0 86 178 9871
Biso mean--17.31 10.12 -
Num. residues----1183
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0199958
X-RAY DIFFRACTIONr_bond_other_d0.0020.029148
X-RAY DIFFRACTIONr_angle_refined_deg1.6491.95413507
X-RAY DIFFRACTIONr_angle_other_deg1.047321052
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.19551177
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.04824.333510
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.406151634
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4691548
X-RAY DIFFRACTIONr_chiral_restr0.0960.21414
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02111300
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022396
X-RAY DIFFRACTIONr_mcbond_it0.9331.624732
X-RAY DIFFRACTIONr_mcbond_other0.9331.624730
X-RAY DIFFRACTIONr_mcangle_it1.6012.4245901
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 122 -
Rwork0.243 2489 -
all-2611 -
obs--79.68 %

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