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- PDB-2onb: Human Thymidylate Synthase at low salt conditions with PDPA bound -

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Basic information

Entry
Database: PDB / ID: 2onb
TitleHuman Thymidylate Synthase at low salt conditions with PDPA bound
ComponentsThymidylate synthetase
KeywordsTRANSFERASE / diphosphonic acid / FdUMP / ZD9331 / heteroinhibition
Function / homology
Function and homology information


: / modulation by virus of host process / uracil metabolic process / : / response to organophosphorus / response to xenobiotic stimulus => GO:0009410 / intestinal epithelial cell maturation / tetrahydrofolate metabolic process / response to folic acid / Interconversion of nucleotide di- and triphosphates ...: / modulation by virus of host process / uracil metabolic process / : / response to organophosphorus / response to xenobiotic stimulus => GO:0009410 / intestinal epithelial cell maturation / tetrahydrofolate metabolic process / response to folic acid / Interconversion of nucleotide di- and triphosphates / response to vitamin A / thymidylate synthase / sequence-specific mRNA binding / cartilage development / tetrahydrofolate interconversion / thymidylate synthase activity / folic acid binding / dTMP biosynthetic process / dTTP biosynthetic process / G1/S-Specific Transcription / DNA biosynthetic process / developmental growth / response to glucocorticoid / mRNA regulatory element binding translation repressor activity / response to progesterone / response to cytokine / liver regeneration / response to toxic substance / circadian rhythm / regulation of translation / methylation / response to ethanol / mitochondrial inner membrane / negative regulation of translation / mitochondrial matrix / response to xenobiotic stimulus / mRNA binding / nucleolus / protein homodimerization activity / mitochondrion / nucleus / cytosol / 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
PROPANE-1,3-DIYLBIS(PHOSPHONIC ACID) / Thymidylate synthase / Thymidylate synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsLovelace, L.L. / Gibson, L.M. / Lebioda, L.
CitationJournal: Biochemistry / Year: 2007
Title: Cooperative Inhibition of Human Thymidylate Synthase by Mixtures of Active Site Binding and Allosteric Inhibitors
Authors: Lovelace, L.L. / Gibson, L.M. / Lebioda, L.
History
DepositionJan 23, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _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 synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4304
Polymers36,0671
Non-polymers3623
Water1,53185
1
A: Thymidylate synthetase
hetero molecules

A: Thymidylate synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,8598
Polymers72,1352
Non-polymers7246
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+2/31
Buried area5870 Å2
ΔGint-25 kcal/mol
Surface area21680 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)95.690, 95.690, 82.503
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Thymidylate synthetase


Mass: 36067.402 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q53Y97, UniProt: P04818*PLUS
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-7PA / PROPANE-1,3-DIYLBIS(PHOSPHONIC ACID)


Mass: 204.055 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H10O6P2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 85 / 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: 3.02 Å3/Da / Density % sol: 59.29 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 30 mM ammonium sulfate, 30 mM 40% PEG 4K, 0.1 M Tris pH 8.5, 20 mM 2-ME, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 0.97251
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 20, 2004
RadiationMonochromator: two passes, half degree / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97251 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 12337 / % possible obs: 100 % / Redundancy: 18.2 % / Rmerge(I) obs: 0.109 / Χ2: 1.72 / Net I/σ(I): 8.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.7-2.817.30.33412260.7491100
2.8-2.9118.60.27311970.8251100
2.91-3.0418.90.2312070.8561100
3.04-3.218.90.17812291.0231100
3.2-3.418.90.1512161.3221100
3.4-3.6618.60.12712201.8411100
3.66-4.0318.40.11212352.2771100
4.03-4.6218.10.09112342.7191100
4.62-5.81180.08712502.6461100
5.81-5016.70.07313232.945199.8

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNS1.1refinement
PDB_EXTRACT2data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1YPV

1ypv


Resolution: 2.7→41.44 Å / Rfactor Rfree error: 0.007 / FOM work R set: 0.814 / Data cutoff high absF: 211861.516 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.259 1253 10.3 %RANDOM
Rwork0.216 ---
obs-12144 98.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 53.34 Å2 / ksol: 0.363 e/Å3
Displacement parametersBiso mean: 52.5 Å2
Baniso -1Baniso -2Baniso -3
1--5.74 Å20.76 Å20 Å2
2---5.74 Å20 Å2
3---11.49 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.45 Å0.34 Å
Refinement stepCycle: LAST / Resolution: 2.7→41.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2097 0 20 85 2202
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23.7
X-RAY DIFFRACTIONc_improper_angle_d1.03
X-RAY DIFFRACTIONc_mcbond_it1.551.5
X-RAY DIFFRACTIONc_mcangle_it2.732
X-RAY DIFFRACTIONc_scbond_it1.962
X-RAY DIFFRACTIONc_scangle_it2.992.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 25

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
2.7-2.740.373350.282408443
2.74-2.780.388450.301419464
2.78-2.820.392430.267431474
2.82-2.860.336490.288412461
2.86-2.910.358470.278421468
2.91-2.960.265500.245421471
2.96-3.010.38440.254438482
3.01-3.070.315480.269426474
3.07-3.130.295500.252428478
3.13-3.20.283470.249430477
3.2-3.280.34400.24440480
3.28-3.360.249520.222424476
3.36-3.450.292540.227445499
3.45-3.550.219380.225446484
3.55-3.660.275450.217436481
3.66-3.80.284550.222434489
3.8-3.950.255560.21443499
3.95-4.130.218600.19425485
4.13-4.340.217560.155454510
4.34-4.620.195500.169435485
4.62-4.970.239530.173440493
4.97-5.470.307560.229448504
5.47-6.270.233680.249436504
6.27-7.890.262620.246454516
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramHicupprotein.topHIcup
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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