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- PDB-1f4e: CRYSTAL STRUCTURE OF E. COLI THYMIDYLATE SYNTHASE COMPLEXED WITH ... -

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Basic information

Entry
Database: PDB / ID: 1f4e
TitleCRYSTAL STRUCTURE OF E. COLI THYMIDYLATE SYNTHASE COMPLEXED WITH TOSYL-D-PROLINE
ComponentsTHYMIDYLATE SYNTHASE
KeywordsTRANSFERASE / Crystal Structure of E. Coli Thymidylate Synthase Complexed with Tosyl-D-Proline
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
TOSYL-D-PROLINE / Thymidylate synthase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsErlanson, D.A. / Braisted, A.C. / Raphael, D.R. / Randal, M. / Stroud, R.M. / Gordon, E. / Wells, J.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2000
Title: Site-directed ligand discovery.
Authors: Erlanson, D.A. / Braisted, A.C. / Raphael, D.R. / Randal, M. / Stroud, R.M. / Gordon, E.M. / Wells, J.A.
History
DepositionJun 7, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 22, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.pdbx_details
Revision 1.5Feb 28, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.6Nov 3, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_special_symmetry ...database_2 / pdbx_struct_special_symmetry / 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
Revision 1.7Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: THYMIDYLATE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,75910
Polymers30,5601
Non-polymers1,1999
Water3,945219
1
A: THYMIDYLATE SYNTHASE
hetero molecules

A: THYMIDYLATE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,51820
Polymers61,1192
Non-polymers2,39818
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation16_566x,-y+1,-z+3/21
Buried area7300 Å2
ΔGint-117 kcal/mol
Surface area21320 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)131.880, 131.880, 131.880
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number199
Space group name H-MI213
Components on special symmetry positions
IDModelComponents
11A-413-

HOH

DetailsThe biological assembly is a dimer constructed from chain A and a symmetry partner generated by the two-fold

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Components

#1: Protein THYMIDYLATE SYNTHASE


Mass: 30559.666 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / Strain (production host): C2913 / References: UniProt: P0A884, thymidylate synthase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-TPR / TOSYL-D-PROLINE


Mass: 269.317 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H15NO4S
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 219 / 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: 3.1 Å3/Da / Density % sol: 61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 2.0 M ammonium sulphate, 20 mM potassium phosphate, 0.2 M EDTA, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 20.0K
Crystal grow
*PLUS
Method: vapor diffusion
Details: Perry, K.M., (1990) Proteins: Struct.,Funct., Genet., 8, 315.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12.5 mg/mlthymidylate synthases1drop
20.2 mMEDTA1drop
31 mMdithiothreitol1drop
420 mMpotassium phosphate1drop
51.15 mMammonium sulfate1drop
62.3 Mammonium sulfate1reservoir
70.2 mMEDTA1reservoir
81 mMdithiothreitol1reservoir
920 mMpotassium phisphate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 10, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→10 Å / Num. all: 31422 / Num. obs: 31422 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Biso Wilson estimate: 28.5 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 19.7
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 3.8 / Num. unique all: 2822 / % possible all: 99.5
Reflection
*PLUS
% possible obs: 100 % / Num. measured all: 202300
Reflection shell
*PLUS
% possible obs: 100 % / Rmerge(I) obs: 0.282

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Processing

Software
NameClassification
AMoREphasing
REFMACrefinement
d*TREKdata scaling
RefinementResolution: 1.9→10 Å / SU B: 3.66 / SU ML: 0.104 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.135 / ESU R Free: 0.136 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.238 1519 5 %random
Rwork0.192 ---
all0.194 31422 --
obs0.194 31422 99.9 %-
Displacement parametersBiso mean: 36.7 Å2
Refinement stepCycle: LAST / Resolution: 1.9→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2153 0 74 219 2446
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0110.02
X-RAY DIFFRACTIONp_angle_d0.0310.04
X-RAY DIFFRACTIONp_planar_d0.040.05
X-RAY DIFFRACTIONp_mcbond_it1.42
X-RAY DIFFRACTIONp_mcangle_it2.13
X-RAY DIFFRACTIONp_scbond_it1.82
X-RAY DIFFRACTIONp_scangle_it2.93
X-RAY DIFFRACTIONp_chiral_restr0.1090.15
X-RAY DIFFRACTIONp_singtor_nbd0.1760.3
X-RAY DIFFRACTIONp_multtor_nbd0.250.3
X-RAY DIFFRACTIONp_xyhbond_nbd0.140.3
X-RAY DIFFRACTIONp_planar_tor3.87
X-RAY DIFFRACTIONp_staggered_tor14.515
X-RAY DIFFRACTIONp_transverse_tor29.920
X-RAY DIFFRACTIONp_special_tor015
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.9 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.192
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 36.7 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_mcbond_it1.42
X-RAY DIFFRACTIONp_scbond_it1.82
X-RAY DIFFRACTIONp_mcangle_it2.13
X-RAY DIFFRACTIONp_scangle_it2.93

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