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- PDB-7jxf: E. coli TSase complex with a bi-substrate reaction intermediate d... -

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Basic information

Entry
Database: PDB / ID: 7jxf
TitleE. coli TSase complex with a bi-substrate reaction intermediate diastereomer 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
5-HYDROXYMETHYLURIDINE-2'-DEOXY-5'-MONOPHOSPHATE / Chem-VMV / Chem-VNM / Thymidylate synthase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsFiner-Moore, J. / Kholodar, S.A. / Stroud, R.M. / Kohen, A. / Moliner, V. / Swiderek, K.
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.USA / 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 27, 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 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / 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)62,7348
Polymers61,1192
Non-polymers1,6146
Water7,386410
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5610 Å2
ΔGint-45 kcal/mol
Surface area19530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.442, 125.442, 67.049
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, 416 molecules

#2: Chemical ChemComp-5HU / 5-HYDROXYMETHYLURIDINE-2'-DEOXY-5'-MONOPHOSPHATE


Type: DNA linking / Mass: 338.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N2O9P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-VMV / N-[4-({[(6S)-2,4-diamino-5,6,7,8-tetrahydropyrido[3,2-d]pyrimidin-6-yl]methyl}amino)benzene-1-carbonyl]-L-glutamic acid


Mass: 443.456 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H25N7O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-VNM / (2S)-2-({4-[({(6S)-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
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 410 / 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: 2.49 Å3/Da / Density % sol: 50.63 % / Description: hexagonal rods
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.1
Details: 8mg/ml protein, 3.3 mM inhibitor, 5mM DTT against 1.35 M NaCitrate, 0.1 M Hepes, pH7.1
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: Dec 3, 2017
RadiationMonochromator: double Xtal SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.116 Å / Relative weight: 1
ReflectionResolution: 1.5→108.64 Å / Num. obs: 88818 / % possible obs: 92.7 % / Redundancy: 15.738 % / Biso Wilson estimate: 25.38 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.05 / Rrim(I) all: 0.052 / Χ2: 1.062 / Net I/σ(I): 26.24
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.5-1.544.4682.1520.538530.1962.42954.7
1.54-1.585.5131.6660.7849380.2981.84171.6
1.58-1.636.8641.3181.1755030.4571.42782.8
1.63-1.688.3540.991.7759710.6781.05691.5
1.68-1.7310.3350.8072.5161910.7980.84998.6
1.73-1.813.840.5614.3360880.9320.58399.9
1.8-1.8619.5230.3917.5758780.9780.401100
1.86-1.9420.6170.27311.1756460.990.28100
1.94-2.0320.1310.19115.7454680.9950.195100
2.03-2.1219.6060.14420.4251760.9970.148100
2.12-2.2420.9250.10828.149880.9980.11100
2.24-2.3720.4050.08834.8746360.9990.09100
2.37-2.5419.3160.07639.3944060.9990.078100
2.54-2.7420.8070.06150.541290.9990.062100
2.74-320.1480.04961.6137720.9990.051100
3-3.3618.5160.0472.36343010.041100
3.36-3.8819.6390.03187.73302810.032100
3.88-4.7518.3220.02793.43256810.028100
4.75-6.7219.1920.02893.4320170.9990.029100
6.72-108.6417.6740.02395.1311320.9990.02499.9

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Processing

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

6nnr


Resolution: 1.5→108.64 Å / SU ML: 0.1819 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.8028
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1748 1999 2.27 %
Rwork0.1513 86136 -
obs0.1518 88135 91.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.61 Å2
Refinement stepCycle: LAST / Resolution: 1.5→108.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4290 0 110 410 4810
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00874908
X-RAY DIFFRACTIONf_angle_d1.26076730
X-RAY DIFFRACTIONf_chiral_restr0.0866693
X-RAY DIFFRACTIONf_plane_restr0.0074876
X-RAY DIFFRACTIONf_dihedral_angle_d20.54241822
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.540.3119710.33952901X-RAY DIFFRACTION43.53
1.54-1.580.34881020.31174621X-RAY DIFFRACTION69.18
1.58-1.630.34621280.2825490X-RAY DIFFRACTION82.3
1.63-1.680.29141400.23646078X-RAY DIFFRACTION90.84
1.68-1.740.25611560.21556566X-RAY DIFFRACTION98.72
1.74-1.810.20231560.18946686X-RAY DIFFRACTION99.88
1.81-1.890.19661540.17376655X-RAY DIFFRACTION100
1.89-1.990.19571540.16326700X-RAY DIFFRACTION100
1.99-2.110.19111540.15766705X-RAY DIFFRACTION100
2.11-2.280.1591580.14836706X-RAY DIFFRACTION100
2.28-2.510.17041560.14976698X-RAY DIFFRACTION100
2.51-2.870.19611540.15446715X-RAY DIFFRACTION100
2.87-3.620.1551560.14016752X-RAY DIFFRACTION100
3.62-108.640.14851600.12566863X-RAY DIFFRACTION99.97
Refinement TLS params.Method: refined / Origin x: -8.29559278027 Å / Origin y: 39.5249463849 Å / Origin z: 11.6949774646 Å
111213212223313233
T0.162715487625 Å20.00653992884464 Å2-0.0328448428267 Å2-0.174765645994 Å20.0198341312262 Å2--0.183966435037 Å2
L0.854465569186 °20.0597319058596 °2-0.223426112021 °2-0.795026938741 °2-0.265709480134 °2--0.677086655508 °2
S0.0181190635346 Å °0.0466184336579 Å °0.154922856513 Å °-0.0559937297952 Å °0.027931568861 Å °0.108035777147 Å °-0.00479728592788 Å °-0.0725557969799 Å °-0.0373652886257 Å °
Refinement TLS groupSelection details: ALL

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