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- PDB-1aiq: CRYSTAL STRUCTURE OF THYMIDYLATE SYNTHASE R126E MUTANT -

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Basic information

Entry
Database: PDB / ID: 1aiq
TitleCRYSTAL STRUCTURE OF THYMIDYLATE SYNTHASE R126E MUTANT
ComponentsTHYMIDYLATE SYNTHASE
KeywordsTRANSFERASE / METHYLTRANSFERASE
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
10-PROPARGYL-5,8-DIDEAZAFOLIC ACID / 2'-DEOXYURIDINE 5'-MONOPHOSPHATE / Thymidylate synthase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR / Resolution: 2.2 Å
AuthorsStrop, P. / Montfort, W.R.
CitationJournal: Protein Sci. / Year: 1997
Title: Crystal structures of a marginally active thymidylate synthase mutant, Arg 126-->Glu.
Authors: Strop, P. / Changchien, L. / Maley, F. / Montfort, W.R.
History
DepositionApr 23, 1997Processing site: BNL
Revision 1.0Nov 12, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Apr 18, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.4Nov 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_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 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
B: THYMIDYLATE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,6346
Polymers61,0632
Non-polymers1,5714
Water3,171176
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7660 Å2
ΔGint-24 kcal/mol
Surface area19130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.610, 126.610, 67.300
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: Protein THYMIDYLATE SYNTHASE / TRANSFERASE


Mass: 30531.584 Da / Num. of mol.: 2 / Mutation: R126E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: BLUSCRIPT SK+ / Production host: Escherichia coli (E. coli) / Strain (production host): XAC25 THY- STRAIN / 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-CB3 / 10-PROPARGYL-5,8-DIDEAZAFOLIC ACID


Mass: 477.469 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H23N5O6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 176 / 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: 2.55 Å3/Da / Density % sol: 52 %
Crystal growpH: 8 / Details: 2.4M AMMONIUM SULFATE, 20MM, pH 8.0
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Details: drop contained 1:1 mixture of protein and precipitant
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlR126E TS1drop
23 mMdUMP1drop
33 mMCB37171drop
420 mMpotassium phosphate1drop
52.5 Mammonium sulfate1reservoirprecipitant
620 mMpotassium phosphate1reservoirprecipitant
74 mMdithiothreitol1reservoirprecipitant

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.5418
DetectorType: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER / Date: Dec 1, 1995
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. obs: 33337 / % possible obs: 92 % / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Rsym value: 0.052
Reflection shellResolution: 2.2→2.5 Å / Mean I/σ(I) obs: 2.2 / Rsym value: 0.22 / % possible all: 75
Reflection
*PLUS
Num. measured all: 121313 / Rmerge(I) obs: 0.052
Reflection shell
*PLUS
% possible obs: 75 % / Rmerge(I) obs: 0.22

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Processing

Software
NameVersionClassification
AMoREphasing
TNT5Erefinement
PROCORdata reduction
FBSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR / Resolution: 2.2→20 Å / Isotropic thermal model: TNT BCORREL / σ(F): 2 / Stereochemistry target values: TNT PROTGEO
RfactorNum. reflection% reflection
Rwork0.163 --
obs-29307 90 %
Solvent computationBsol: 143.2 Å2 / ksol: 0.657 e/Å3
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4302 0 110 176 4588
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.00945390.8
X-RAY DIFFRACTIONt_angle_deg1.00961241.3
X-RAY DIFFRACTIONt_dihedral_angle_d18.78525640
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.0061262
X-RAY DIFFRACTIONt_gen_planes0.0136385
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd0.0224310
Software
*PLUS
Name: TNT / Version: 5E / Classification: refinement
Refine LS restraints
*PLUS
Type: t_plane_restr / Dev ideal: 0.013 / Weight: 5

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