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- PDB-2g86: L. casei thymidylate synthase Y261F in complex with substrate, dUMP -

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Basic information

Entry
Database: PDB / ID: 2g86
TitleL. casei thymidylate synthase Y261F in complex with substrate, dUMP
ComponentsThymidylate synthase
KeywordsTRANSFERASE / dUMP-binding residue / dUMP complex / thymidylate synthase mutant
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/dCMP hydroxymethylase / Thymidylate synthase, active site / Thymidylate synthase active site. / Thymidylate synthase / Thymidylate synthase/dCMP hydroxymethylase domain / Thymidylate synthase/dCMP hydroxymethylase superfamily / Thymidylate synthase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
2'-DEOXYURIDINE 5'-MONOPHOSPHATE / Thymidylate synthase
Similarity search - Component
Biological speciesLactobacillus casei (bacteria)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.4 Å
AuthorsFiner-Moore, J.S. / Stroud, R.M.
CitationJournal: Biochemistry / Year: 2006
Title: The role of protein dynamics in thymidylate synthase catalysis: variants of conserved 2'-deoxyuridine 5'-monophosphate (dUMP)-binding Tyr-261
Authors: Newby, Z. / Lee, T.T. / Morse, R.J. / Liu, Y. / Liu, L. / Venkatraman, P. / Santi, D.V. / Finer-Moore, J.S. / Stroud, R.M.
History
DepositionMar 1, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)36,9232
Polymers36,6141
Non-polymers3081
Water1,63991
1
A: Thymidylate synthase
hetero molecules

A: Thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,8454
Polymers73,2292
Non-polymers6162
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_554-x+y,y,-z-1/21
Buried area5850 Å2
ΔGint-22 kcal/mol
Surface area26400 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)78.550, 78.550, 241.800
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
DetailsBiological assembly is a dimer. Second half of the dimer is generated by the crystallographic two-fold axis according to the following transformation: -x+y, y, -1/2-z

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Components

#1: Protein Thymidylate synthase / / TS / TSase


Mass: 36614.453 Da / Num. of mol.: 1 / Mutation: Y261F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus casei (bacteria) / Gene: thyA / Plasmid: pSCTS9 / Production host: Escherichia coli (E. coli) / Strain (production host): Chi2913recA / References: UniProt: P00469, thymidylate synthase
#2: Chemical ChemComp-UMP / 2'-DEOXYURIDINE 5'-MONOPHOSPHATE / DUMP / Deoxyuridine monophosphate


Mass: 308.182 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H13N2O8P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 91 / Source method: isolated from a natural source / Formula: H2O

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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: 2.94 Å3/Da / Density % sol: 58.15 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: vapor diffusion against 20mM KPO4 buffer; protein solution in same buffer with 15-20mM ammonium sulfate, DTT, 38 mMdUMP, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Jan 1, 1996
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.4→39.4 Å / Num. all: 16639 / Num. obs: 16639 / % possible obs: 91.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 29 Å2 / Net I/σ(I): 17.4
Reflection shellResolution: 2.4→2.55 Å / % possible all: 87.5

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Processing

Software
NameVersionClassification
CNS1.1refinement
CCP4(TRUNCATE)data scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.4→39.4 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2187162.82 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.233 1672 10 %RANDOM
Rwork0.174 ---
all0.177 16639 --
obs0.174 16639 91.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 56.8833 Å2 / ksol: 0.352468 e/Å3
Displacement parametersBiso mean: 42.8 Å2
Baniso -1Baniso -2Baniso -3
1--1.09 Å21.23 Å20 Å2
2---1.09 Å20 Å2
3---2.17 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.36 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 2.4→39.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2592 0 20 91 2703
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.022
X-RAY DIFFRACTIONc_angle_deg2.2
X-RAY DIFFRACTIONc_dihedral_angle_d26.3
X-RAY DIFFRACTIONc_improper_angle_d2.09
X-RAY DIFFRACTIONc_mcbond_it1.341.5
X-RAY DIFFRACTIONc_mcangle_it2.32
X-RAY DIFFRACTIONc_scbond_it2.962
X-RAY DIFFRACTIONc_scangle_it4.062.5
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.324 250 9.7 %
Rwork0.215 2317 -
obs--87.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3paramed.ligump_po4.topo

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