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- PDB-2tsc: STRUCTURE, MULTIPLE SITE BINDING, AND SEGMENTAL ACCOMODATION IN T... -

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Basic information

Entry
Database: PDB / ID: 2tsc
TitleSTRUCTURE, MULTIPLE SITE BINDING, AND SEGMENTAL ACCOMODATION IN THYMIDYLATE SYNTHASE ON BINDING D/UMP AND AN ANTI-FOLATE
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 / Resolution: 1.97 Å
AuthorsMontfort, W.R. / Stroud, R.M.
Citation
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.
#1: Journal: Biochemistry / Year: 1990
Title: Pairwise Specificity and Sequential Binding in Enzyme Catalysis: Thymidylate Synthase
Authors: Finer-Moore, J.S. / Montfort, W.R. / Stroud, R.M.
#2: Journal: Proteins / Year: 1990
Title: Plastic Adaptation Toward Mutations in Proteins: Structural Comparison of Thymidylate Synthases
Authors: Perry, K.M. / Fauman, E.B. / Finer-Moore, J.S. / Montfort, W.R. / Maley, G.F. / Maley, F. / Stroud, R.M.
History
DepositionJul 3, 1991Processing site: BNL
Revision 1.0Oct 15, 1991Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _pdbx_database_status.process_site / _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 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: THYMIDYLATE SYNTHASE
B: THYMIDYLATE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,4866
Polymers60,9152
Non-polymers1,5714
Water3,567198
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7900 Å2
ΔGint-22 kcal/mol
Surface area19350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.100, 127.100, 67.900
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


Mass: 30457.553 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / 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.: 198 / 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

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Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 52.65 %
Crystal grow
*PLUS
Method: vapor diffusion / pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15-9 mg/mLprotein1drop
220 mMpotasssium1drop
32.3 Mammonium1drop
4100 mMdUMP1drop
54.78 mMCB37171drop
620 mMpotassium1reservoir
70.1 mMdisodium ethylenediaminetetraacetic acid1reservoir
820 mMbeta-mercaptoethanol1reservoir

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Data collection

Reflection
*PLUS
Highest resolution: 1.97 Å / Rmerge(I) obs: 0.18

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 1.97→7.5 Å / Rfactor obs: 0.18
Refinement stepCycle: LAST / Resolution: 1.97→7.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4292 0 110 198 4600
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.022
X-RAY DIFFRACTIONp_angle_d0.059
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.18
Solvent computation
*PLUS
Displacement parameters
*PLUS

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