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- PDB-7jx1: E. coli TSase complex with a bi-substrate reaction intermediate analog -

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Basic information

Entry
Database: PDB / ID: 7jx1
TitleE. coli TSase complex with a bi-substrate reaction intermediate analog
ComponentsThymidylate synthase
KeywordsBIOSYNTHETIC PROTEIN / non covalent intermediate / half-sites activity / TMP synthesis / inhibitor
Function / homology
Function and homology information


thymidylate synthase / thymidylate synthase activity / dTMP biosynthetic process / dTTP biosynthetic process / methylation / cytoplasm
Similarity search - Function
Thymidylate synthase, active site / Thymidylate synthase active site. / Thymidylate synthase / Thymidylate synthase/dCMP hydroxymethylase domain / Thymidylate synthase/dCMP hydroxymethylase superfamily / Thymidylate synthase
Similarity search - Domain/homology
PHOSPHATE ION / THYMIDINE-5'-PHOSPHATE / Chem-VLA / Chem-VLD / Thymidylate synthase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 Å
AuthorsFiner-Moore, J. / Kholodar, S.A. / Stroud, R.M. / Kohen, A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM24485 United States
Citation
Journal: Biochemistry / Year: 2021
Title: Caught in Action: X-ray Structure of Thymidylate Synthase with Noncovalent Intermediate Analog.
Authors: Kholodar, S.A. / Finer-Moore, J.S. / Swiderek, K. / Arafet, K. / Moliner, V. / Stroud, R.M. / Kohen, A.
#1: Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Parallel reaction pathways and noncovalent intermediates in thymidylate synthase revealed by experimental and computational tools.
Authors: Kholodar, S.A. / Ghosh, A.K. / Swiderek, K. / Moliner, V. / Kohen, A.
History
DepositionAug 26, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 21, 2021Provider: repository / Type: Initial release
Revision 1.1May 5, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Dec 25, 2024Group: Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _pdbx_entry_details.has_protein_modification

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,7426
Polymers61,1192
Non-polymers1,6224
Water4,738263
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5460 Å2
ΔGint-28 kcal/mol
Surface area19350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.980, 125.980, 67.340
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Space group name HallP6c
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/2
#3: y,-x+y,z+1/2
#4: -y,x-y,z
#5: -x+y,-x,z
#6: -x,-y,z+1/2

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Thymidylate synthase / TSase


Mass: 30559.666 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: thyA / Production host: Escherichia coli (E. coli) / References: UniProt: A0A029ILG4, thymidylate synthase

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Non-polymers , 5 types, 267 molecules

#2: Chemical ChemComp-VLA / N-(4-{[(2,4-diamino-7,8-dihydropyrido[3,2-d]pyrimidin-6-yl)methyl]amino}benzene-1-carbonyl)-L-glutamic acid


Mass: 441.441 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H23N7O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-TMP / THYMIDINE-5'-PHOSPHATE


Mass: 322.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N2O8P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-VLD / (2S)-2-({4-[({(6R)-2,4-diamino-5-[(1-{(2R,4S,5R)-4-hydroxy-5-[(phosphonooxy)methyl]tetrahydrofuran-2-yl}-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl)methyl]-5,6,7,8-tetrahydropyrido[3,2-d]pyrimidin-6-yl}methyl)amino]benzoyl}amino)pentanedioic acid (non-preferred name)


Mass: 763.649 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H38N9O13P / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 263 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.52 Å3/Da / Density % sol: 51.27 % / Description: hexagonal rods
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 5.5 mg/ml protein, 3.3 mM inhibitor and 5 mM DTT against 1.3M NaCitrate, 0.1M Hepes pH7.5
PH range: 7.1-7.6

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Data collection

DiffractionMean temperature: 173 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.116 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 19, 2019
RadiationMonochromator: double crystal SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.116 Å / Relative weight: 1
ReflectionResolution: 1.82→109.1 Å / Num. obs: 53762 / % possible obs: 98.1 % / Redundancy: 17.738 % / Biso Wilson estimate: 35.33 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.103 / Rrim(I) all: 0.106 / Χ2: 1.112 / Net I/σ(I): 17.34
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRrim(I) all% possible allCC1/2
1.82-1.877.3353.4690.5430853.72776.8
1.87-1.929.5312.660.8838392.81497.40.283
1.92-1.9711.641.8581.4237941.94599.90.532
1.97-2.0315.1561.3632.2937401.4111000.749
2.03-2.120.0181.0323.6336071.0591000.878
2.1-2.1720.7730.7695.0734830.7881000.938
2.17-2.2620.4370.596.533560.6051000.96
2.26-2.3519.4530.4618.0832320.4741000.974
2.35-2.4520.4220.3879.6430990.3961000.987
2.45-2.5720.9560.28812.6229760.2951000.99
2.57-2.7120.4920.22715.4828380.2331000.994
2.71-2.8819.3290.16919.8526750.1731000.996
2.88-3.0720.7210.12326.4925420.1261000.998
3.07-3.3220.7280.09135.423430.0931000.999
3.32-3.6419.6510.06545.421610.0671000.999
3.64-4.0719.7970.05354.5519730.0551000.999
4.07-4.720.4390.04364.1517240.0451000.999
4.7-5.7518.790.04558.9114810.0461001
5.75-8.1420.6860.04360.9211510.0441001
8.14-109.118.7390.0369.66630.0311000.999

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
PHENIX1.17.1_3660phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6NNR

6nnr


Resolution: 1.82→109.1 Å / SU ML: 0.2555 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.4574
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.19 1984 3.72 %
Rwork0.1507 51326 -
obs0.1522 53310 97.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.84 Å2
Refinement stepCycle: LAST / Resolution: 1.82→109.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4293 0 164 263 4720
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01174916
X-RAY DIFFRACTIONf_angle_d1.26736
X-RAY DIFFRACTIONf_chiral_restr0.0608694
X-RAY DIFFRACTIONf_plane_restr0.0073882
X-RAY DIFFRACTIONf_dihedral_angle_d19.274706
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.82-1.860.4259930.38662484X-RAY DIFFRACTION66.47
1.86-1.920.36431410.33343620X-RAY DIFFRACTION96.58
1.92-1.970.29651420.25913738X-RAY DIFFRACTION99.67
1.97-2.040.27781420.20383750X-RAY DIFFRACTION100
2.04-2.110.23251470.17343721X-RAY DIFFRACTION100
2.11-2.190.19651460.16023776X-RAY DIFFRACTION100
2.19-2.290.21861460.15023730X-RAY DIFFRACTION100
2.29-2.410.20331420.14493767X-RAY DIFFRACTION100
2.41-2.560.19781470.14673778X-RAY DIFFRACTION100
2.56-2.760.21041490.15173755X-RAY DIFFRACTION100
2.76-3.040.21471450.15813765X-RAY DIFFRACTION100
3.04-3.480.16091480.14483784X-RAY DIFFRACTION100
3.48-4.380.14231420.1153780X-RAY DIFFRACTION100
4.39-109.10.17741540.14243878X-RAY DIFFRACTION99.95
Refinement TLS params.Method: refined / Origin x: -30.2851564271 Å / Origin y: 27.1076045271 Å / Origin z: -11.3719295773 Å
111213212223313233
T0.236284843056 Å2-0.00279844005891 Å2-0.004913272418 Å2-0.231244666841 Å2-0.0275280638549 Å2--0.242470302441 Å2
L0.764796473465 °20.0746801224885 °2-0.255304030591 °2-0.753110279503 °20.0781984142217 °2--0.693283317863 °2
S0.0113561401705 Å °-0.0415052977526 Å °0.162742834553 Å °0.0236719955672 Å °0.0115287850184 Å °0.0653490326443 Å °-0.038415474024 Å °0.00262291625139 Å °-0.0257959817407 Å °
Refinement TLS groupSelection details: all

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