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- PDB-4tms: PLASTIC ADAPTATION TOWARD MUTATIONS IN PROTEINS: STRUCTURAL COMPA... -

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Basic information

Entry
Database: PDB / ID: 4tms
TitlePLASTIC ADAPTATION TOWARD MUTATIONS IN PROTEINS: STRUCTURAL COMPARISON OF THYMIDYLATE SYNTHASES
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
PHOSPHATE ION / Thymidylate synthase
Similarity search - Component
Biological speciesLactobacillus casei (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.35 Å
AuthorsFiner-Moore, J. / Stroud, R.
Citation
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.
#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
DepositionJan 7, 1992Processing site: BNL
Revision 1.0Jan 15, 1992Provider: 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 28, 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

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Assembly

Deposited unit
A: THYMIDYLATE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7252
Polymers36,6301
Non-polymers951
Water70339
1
A: THYMIDYLATE SYNTHASE
hetero molecules

A: THYMIDYLATE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,4514
Polymers73,2612
Non-polymers1902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_554-x+y,y,-z-1/21
Buried area5190 Å2
ΔGint-29 kcal/mol
Surface area26070 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)78.300, 78.300, 243.200
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: 36630.453 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-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / 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: 58.11 %
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12.5 mg/mlthymidylate synthases1drop
21 mMEDTA1drop
31 mMdithiothreitol1drop
420 mMpotassium phosphate1drop
51.15 Mammonium sulfate1drop
62.3 Mammonium sulfate1reservoir
70.2 mMEDTA1reservoir
81 mMdithiothreitol1reservoir
920 mMpotassium phisphate1reservoir

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Data collection

Reflection
*PLUS
Highest resolution: 2.08 Å / Lowest resolution: 9999 Å / Num. obs: 22275 / % possible obs: 90.5 % / Num. measured all: 66941

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 2.35→7 Å / Rfactor obs: 0.193
Refinement stepCycle: LAST / Resolution: 2.35→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2590 0 5 39 2634
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.018
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg3.6
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
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 7 Å / Rfactor obs: 0.193
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: p_angle_d

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