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- PDB-1f4b: CRYSTAL STRUCTURE OF ESCHERICHIA COLI THYMIDYLATE SYNTHASE -

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Basic information

Entry
Database: PDB / ID: 1f4b
TitleCRYSTAL STRUCTURE OF ESCHERICHIA COLI THYMIDYLATE SYNTHASE
ComponentsTHYMIDYLATE SYNTHASE
KeywordsTRANSFERASE / E. coli thymidylate synthase
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
Thymidylate synthase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 1.75 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 / _exptl_crystal_grow.temp
Revision 1.5Nov 3, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 1.6Oct 16, 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)31,0326
Polymers30,5601
Non-polymers4725
Water4,720262
1
A: THYMIDYLATE SYNTHASE
hetero molecules

A: THYMIDYLATE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,06412
Polymers61,1192
Non-polymers94510
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation16_566x,-y+1,-z+3/21
Buried area6620 Å2
ΔGint-90 kcal/mol
Surface area21190 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)131.170, 131.170, 131.170
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-306-

HOH

21A-309-

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) / Plasmid: PTHYAWT / 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.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 262 / 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: 3.09 Å3/Da / Density % sol: 60 %
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
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: Dec 5, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.75→10 Å / Num. all: 36586 / Num. obs: 36586 / % possible obs: 96.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Biso Wilson estimate: 31.9 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 20.5
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 2 % / Rmerge(I) obs: 0.338 / Mean I/σ(I) obs: 4 / Num. unique all: 3443 / % possible all: 91.6
Reflection
*PLUS
Num. measured all: 104019
Reflection shell
*PLUS
% possible obs: 91.6 %

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Processing

Software
NameClassification
REFMACrefinement
d*TREKdata scaling
RefinementResolution: 1.75→10 Å / SU B: 2.84 / SU ML: 0.089 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.11 / ESU R Free: 0.12 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.244 1838 5 %random
Rwork0.198 ---
all0.2 36586 --
obs0.2 36586 96.7 %-
Displacement parametersBiso mean: 37.15 Å2
Refinement stepCycle: LAST / Resolution: 1.75→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2153 0 27 262 2442
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.010.02
X-RAY DIFFRACTIONp_angle_d0.0290.04
X-RAY DIFFRACTIONp_planar_d0.0370.05
X-RAY DIFFRACTIONp_mcbond_it1.32
X-RAY DIFFRACTIONp_mcangle_it1.953
X-RAY DIFFRACTIONp_scbond_it1.722
X-RAY DIFFRACTIONp_scangle_it2.733
X-RAY DIFFRACTIONp_chiral_restr0.1090.15
X-RAY DIFFRACTIONp_singtor_nbd0.1780.3
X-RAY DIFFRACTIONp_multtor_nbd0.2420.3
X-RAY DIFFRACTIONp_xhyhbond_nbd0.1550.3
X-RAY DIFFRACTIONp_xyhbond_nbd0.1550.3
X-RAY DIFFRACTIONp_planar_tor3.77
X-RAY DIFFRACTIONp_staggered_tor15.315
X-RAY DIFFRACTIONp_transverse_tor29.920
X-RAY DIFFRACTIONp_special_tor015
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
σ(F): 0 / Rfactor all: 0.2 / Rfactor obs: 0.198
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_mcbond_it1.32
X-RAY DIFFRACTIONp_scbond_it1.722
X-RAY DIFFRACTIONp_mcangle_it1.953
X-RAY DIFFRACTIONp_scangle_it2.733

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