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

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Basic information

Entry
Database: PDB / ID: 1ajm
TitleCRYSTAL STRUCTURE OF THYMIDYLATE SYNTHASE R126E MUTANT
ComponentsTHYMIDYLATE SYNTHASE
KeywordsMETHYLTRANSFERASE / TRANSFERASE / DUMP
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: 2.4 Å
AuthorsStrop, P. / Montfort, W.R.
Citation
Journal: 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.
#1: Journal: Biochemistry / Year: 1990
Title: Structure, Multiple Site Binding, and Segmental Accommodation in Thymidylate Synthase on Binding Dump and an Anti-Folate
Authors: Montfort, W.R. / Perry, K.M. / Fauman, E.B. / Finer-Moore, J.S. / Maley, G.F. / Hardy, L. / Maley, F. / Stroud, R.M.
#2: Journal: Biochemistry / Year: 1990
Title: Erratum. Structure, Multiple Site Binding, and Segmental Accommodation in Thymidylate Synthase on Binding Dump and an Anti-Folate
Authors: Montfort, W.R. / Perry, K.M. / Fauman, E.B. / Finer-Moore, J.S. / Maley, G.F. / Hardy, L. / Maley, F. / Stroud, R.M.
History
DepositionMay 6, 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: Derived calculations / Version format compliance
Revision 1.3Apr 18, 2018Group: Data collection / Other / Category: diffrn_detector / pdbx_database_status
Item: _diffrn_detector.detector / _pdbx_database_status.process_site
Revision 1.4Nov 3, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
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
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


Theoretical massNumber of molelcules
Total (without water)30,5321
Polymers30,5321
Non-polymers00
Water90150
1
A: THYMIDYLATE SYNTHASE

A: THYMIDYLATE SYNTHASE


Theoretical massNumber of molelcules
Total (without water)61,0632
Polymers61,0632
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation16_555x,-y,-z+1/21
Buried area4130 Å2
ΔGint-15 kcal/mol
Surface area21090 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)132.700, 132.700, 132.700
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-265-

HOH

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Components

#1: Protein THYMIDYLATE SYNTHASE


Mass: 30531.584 Da / Num. of mol.: 1 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / 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: 3.19 Å3/Da / Density % sol: 61.41 %
Crystal growpH: 7.5 / Details: pH 7.5
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
112 mg/mlR126E TS1drop
23 mMdUMP1drop
320 mMpotassium phosphate1drop
44 mMdithiothreitol1drop
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: 2.4→25 Å / Num. obs: 14066 / % possible obs: 92 % / Observed criterion σ(I): 0 / Redundancy: 6.2 % / Rsym value: 0.101
Reflection
*PLUS
Num. measured all: 88083 / Rmerge(I) obs: 0.101

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Processing

Software
NameVersionClassification
TNT1refinement
PROCORdata reduction
FBSCALEdata scaling
RefinementResolution: 2.4→25 Å / Isotropic thermal model: TNT BCORREL / σ(F): 0 / Stereochemistry target values: TNT PROTGEO
RfactorNum. reflection% reflection
Rwork0.182 --
all-14066 -
obs-14066 92 %
Solvent computationBsol: 157.1 Å2 / ksol: 0.616 e/Å3
Refinement stepCycle: LAST / Resolution: 2.4→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2151 0 0 50 2201
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.01222110.8
X-RAY DIFFRACTIONt_angle_deg1.21729861.3
X-RAY DIFFRACTIONt_dihedral_angle_d19.50512820
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.007632
X-RAY DIFFRACTIONt_gen_planes0.0133165
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd0.021912
Software
*PLUS
Name: TNT / Version: 5E / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg19.5050
X-RAY DIFFRACTIONt_plane_restr0.0135

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