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- PDB-2tdd: STRUCTURES OF THYMIDYLATE SYNTHASE WITH A C-TERMINAL DELETION: RO... -

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Basic information

Entry
Database: PDB / ID: 2tdd
TitleSTRUCTURES OF THYMIDYLATE SYNTHASE WITH A C-TERMINAL DELETION: ROLE OF THE C-TERMINUS IN ALIGNMENT OF D/UMP AND CH2H4FOLATE
ComponentsTHYMIDYLATE SYNTHASE
KeywordsTRANSFERASE (METHYLTRANSFERASE)
Function / homology
Function and homology information


thymidylate synthase / thymidylate synthase activity / dTMP biosynthetic process / dTTP biosynthetic process / methylation / 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
5-HYDROXYMETHYLENE-6-HYDROFOLIC ACID / 5-FLUORO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE / Thymidylate synthase
Similarity search - Component
Biological speciesLactobacillus casei (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.7 Å
AuthorsPerry, K.M. / Carreras, C.W. / Chang, L.C. / Santi, D.V. / Stroud, R.M.
Citation
Journal: Biochemistry / Year: 1993
Title: Structures of thymidylate synthase with a C-terminal deletion: role of the C-terminus in alignment of 2'-deoxyuridine 5'-monophosphate and 5,10-methylenetetrahydrofolate.
Authors: Perry, K.M. / Carreras, C.W. / Chang, L.C. / Santi, D.V. / Stroud, R.M.
#1: Journal: Science / Year: 1987
Title: Atomic Structure of Thymidylate Synthase: Target for Rational Drug Design
Authors: Hardy, L.W. / Finer-Moore, J.S. / Montfort, W.R. / Jones, M.O. / Santi, D.V. / Stroud, R.M.
History
DepositionApr 5, 1993Processing site: BNL
Revision 1.0Jul 15, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 21, 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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: THYMIDYLATE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3313
Polymers36,5311
Non-polymers8002
Water1629
1
A: THYMIDYLATE SYNTHASE
hetero molecules

A: THYMIDYLATE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,6626
Polymers73,0632
Non-polymers1,5994
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_554-x+y,y,-z-1/21
Buried area7650 Å2
ΔGint-26 kcal/mol
Surface area25320 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)78.400, 78.400, 242.200
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein THYMIDYLATE SYNTHASE


Mass: 36531.324 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus casei (bacteria) / References: UniProt: P00469, thymidylate synthase
#2: Chemical ChemComp-THF / 5-HYDROXYMETHYLENE-6-HYDROFOLIC ACID


Mass: 473.439 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H23N7O7
#3: Chemical ChemComp-UFP / 5-FLUORO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE


Type: DNA linking / Mass: 326.172 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H12FN2O8P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.94 Å3/Da / Density % sol: 58.15 %
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
25 mg/mLC-terminal valine1drop
31 %satammonium sulfate1drop
41 mLphosphate1reservoir
55 mg/mLC-terminal valine1reservoir
1phosphate1drop

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Data collection

Reflection
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 9999 Å / Num. obs: 10672 / % possible obs: 83 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.097

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementRfactor Rwork: 0.19 / Highest resolution: 2.7 Å
Details: THE ELECTRON DENSITY FOR THIS STRUCTURE IS POOR IN REGIONS CORRESPONDING TO RESIDUES 21 - 26 AND 90 - 139.
Refinement stepCycle: LAST / Highest resolution: 2.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2580 0 55 9 2644
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.025
X-RAY DIFFRACTIONx_angle_deg3.8
Refinement
*PLUS
Highest resolution: 2.7 Å / Rfactor obs: 0.191
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDType
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_deg

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