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- PDB-1jg0: Crystal structure of Escherichia coli thymidylate synthase comple... -

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Basic information

Entry
Database: PDB / ID: 1jg0
TitleCrystal structure of Escherichia coli thymidylate synthase complexed with 2'-deoxyuridine-5'-monophosphate and N,O-didansyl-L-tyrosine
Componentsthymidylate synthase
KeywordsTRANSFERASE / thymidylate synthase / didansyl tyrosine
Function / homology
Function and homology information


thymidylate synthase / thymidylate synthase activity / dTMP biosynthetic process / dTTP biosynthetic process / response to radiation / regulation of translation / methylation / magnesium ion binding / protein homodimerization activity / RNA binding / 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
N,O-DIDANSYL-L-TYROSINE / 2'-DEOXYURIDINE 5'-MONOPHOSPHATE / Thymidylate synthase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsFritz, T.A. / Tondi, D. / Finer-Moore, J.S. / Costi, M.P. / Stroud, R.M.
Citation
Journal: Chem.Biol. / Year: 2001
Title: Predicting and harnessing protein flexibility in the design of species-specific inhibitors of thymidylate synthase.
Authors: Fritz, T.A. / Tondi, D. / Finer-Moore, J.S. / Costi, M.P. / Stroud, R.M.
#1: Journal: Chem.Biol. / Year: 1999
Title: Structure-based discovery and in- parallel optimization of novel competitive inhibitors of thymidylate synthase
History
DepositionJun 22, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 8, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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

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Assembly

Deposited unit
A: thymidylate synthase
B: thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,6876
Polymers60,7752
Non-polymers1,9124
Water7,170398
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5220 Å2
ΔGint-24 kcal/mol
Surface area22250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.797, 87.062, 127.461
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein thymidylate synthase


Mass: 30387.432 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: Esherichia coli / Production host: Escherichia coli (E. coli) / Strain (production host): X2913 / References: UniProt: P0A884, thymidylate synthase
#2: Chemical ChemComp-UMP / 2'-DEOXYURIDINE 5'-MONOPHOSPHATE / DUMP


Mass: 308.182 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H13N2O8P
#3: Chemical ChemComp-DDT / N,O-DIDANSYL-L-TYROSINE


Mass: 647.761 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C33H33N3O7S2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 398 / Source method: isolated from a natural source / Formula: H2O
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: 2.45 Å3/Da / Density % sol: 49.89 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 18-20% PEG 4000, 0.2 M sodium acetate, 0.1 M Tris, 5 mM dithiothreitol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
16 mg/mlprotein1drop
218-20 %PEG40001drop
30.2 Msodium acetate1drop
40.1 MTris-Cl1droppH8.5
55 mMdithiothreitol1drop
61 mMdUMP1reservoir
70.080 mMDDT1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.98 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 26, 1999
RadiationMonochromator: Si(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2→27.42 Å / Num. all: 41243 / Num. obs: 41069 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 8.1 % / Biso Wilson estimate: 10 Å2 / Rmerge(I) obs: 0.097 / Net I/σ(I): 15.8
Reflection shellResolution: 2→2.07 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.428 / Mean I/σ(I) obs: 4.06 / Num. unique all: 4040 / % possible all: 100
Reflection
*PLUS
Num. measured all: 333240

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Processing

Software
NameVersionClassification
AMoREphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SYN WITH WATER AND LIGANDS REMOVED FROM THE MODEL

1syn


Resolution: 2→27.42 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2140489.74 / Data cutoff high rms absF: 2140489.74 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.25 1513 3.7 %RANDOM
Rwork0.212 ---
all-41243 --
obs-41069 99.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 51.03 Å2 / ksol: 0.332 e/Å3
Displacement parametersBiso mean: 29.7 Å2
Baniso -1Baniso -2Baniso -3
1-14.96 Å20 Å20 Å2
2---5.27 Å20 Å2
3----9.69 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.27 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 2→27.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4264 0 130 398 4792
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_dihedral_angle_d24.3
X-RAY DIFFRACTIONc_improper_angle_d1.32
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.321 241 3.6 %
Rwork0.282 6397 -
obs--98.4 %
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 3.7 % / Rfactor obs: 0.212 / Rfactor Rfree: 0.25
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 28.6 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.32
LS refinement shell
*PLUS
Rfactor Rfree: 0.321 / % reflection Rfree: 3.6 % / Rfactor Rwork: 0.282

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