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- PDB-2g8d: Lactobacillus casei thymidylate synthase Y261W-dUMP complex -

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Basic information

Entry
Database: PDB / ID: 2g8d
TitleLactobacillus casei thymidylate synthase Y261W-dUMP complex
Componentsthymidylate synthase
KeywordsTRANSFERASE / beta sheet / alpha/beta protein / methyltransferase / dUMP complex / active site mutation
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
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 2, 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)36,9622
Polymers36,6531
Non-polymers3081
Water1,44180
1
A: thymidylate synthase
hetero molecules

A: thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,9234
Polymers73,3072
Non-polymers6162
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_554-x+y,y,-z-1/21
Buried area5870 Å2
ΔGint-23 kcal/mol
Surface area25670 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)78.720, 78.720, 242.000
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
DetailsBiological dimer generated by crystallographic two-fold: y-x,y,-1/2-z (applied to fractional coordinates) or -x,y,-121-z (applied to orthogonal angstrom coordinates)

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Components

#1: Protein thymidylate synthase / TS / TSase


Mass: 36653.492 Da / Num. of mol.: 1 / Mutation: Y261W
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 (thy-) / References: UniProt: P00469, thymidylate synthase
#2: Chemical ChemComp-UMP / 2'-DEOXYURIDINE 5'-MONOPHOSPHATE / DUMP


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


Mass: 18.015 Da / Num. of mol.: 80 / 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: 2.95 Å3/Da / Density % sol: 58.32 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Vapor diffusion against 20mM KPO4 buffer from protein solutions in the same buffer, containing 15-20mM ammonium sulfate, DTT and 38mM dUMP, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295.K

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jan 1, 1996
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→39.5 Å / Num. all: 16205 / Num. obs: 16205 / % possible obs: 88.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.088 / Net I/σ(I): 11
Reflection shellResolution: 2.4→2.55 Å / Mean I/σ(I) obs: 2.3 / Num. unique all: 2260 / % possible all: 76.8

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Processing

Software
NameVersionClassification
CNS1.1refinement
CCP4(TRUNCATE)data scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.4→39.47 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 234767.27 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: Arg23 is in two conformations
RfactorNum. reflection% reflectionSelection details
Rfree0.251 1617 10 %RANDOM
Rwork0.186 ---
all0.19 16205 --
obs0.186 16205 88.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 96.6426 Å2 / ksol: 0.359295 e/Å3
Displacement parametersBiso mean: 39 Å2
Baniso -1Baniso -2Baniso -3
1--1.13 Å20.18 Å20 Å2
2---1.13 Å20 Å2
3---2.25 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.61 Å0.42 Å
Refinement stepCycle: LAST / Resolution: 2.4→39.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2595 0 20 80 2695
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.026
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg2.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d2.06
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.491.5
X-RAY DIFFRACTIONc_mcangle_it2.582
X-RAY DIFFRACTIONc_scbond_it3.152
X-RAY DIFFRACTIONc_scangle_it4.322.5
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.38 196 8.7 %
Rwork0.294 2064 -
obs-2260 76.8 %
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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