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- PDB-2vf0: CRYSTAL STRUCTURE OF THE THYMIDYLATE SYNTHASE K48Q COMPLEXED WITH... -

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Basic information

Entry
Database: PDB / ID: 2vf0
TitleCRYSTAL STRUCTURE OF THE THYMIDYLATE SYNTHASE K48Q COMPLEXED WITH 5NO2DUMP AND BW1843U89
ComponentsTHYMIDYLATE SYNTHASE
KeywordsTRANSFERASE / NUCLEOTIDE BIOSYNTHESIS / SUBSTRATE ANOLOGUE / ANTIFOLATE BINDING / RNA-BINDING / METHYLTRANSFERASE / REPRESSOR / BW1843U89 / CYTOPLASM / 5-NO2-DUMP / THYMIDYLATE SYNTHASE / TRANSLATION REGULATION
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
Chem-F89 / 2'-DEOXY-5-NITROURIDINE 5'-MONOPHOSPHATE / Thymidylate synthase
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsSotelo-Mundo, R.R. / Arreola, R. / Maley, F. / Montfort, W.R.
CitationJournal: Int.J.Biochem.Cell Biol. / Year: 2008
Title: Role of an Invariant Lysine Residue in Folate Binding on Escherichia Coli Thymidylate Synthase: Calorimetric and Crystallographic Analysis of the K48Q Mutant.
Authors: Arvizu-Flores, A.A. / Sugich-Miranda, R. / Arreola, R. / Garcia-Orozco, K.D. / Velazquez-Contreras, E.F. / Montfort, W.R. / Maley, F. / Sotelo-Mundo, R.R.
History
DepositionOct 27, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 4, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 12, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)62,9257
Polymers61,1172
Non-polymers1,8075
Water52229
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4930 Å2
ΔGint-26.7 kcal/mol
Surface area24690 Å2
MethodPQS
Unit cell
Length a, b, c (Å)127.160, 127.160, 67.950
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 / TS / TSASE /


Mass: 30558.615 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: MUTANT K48Q COMPLEXED WITH 5-NO2DUMP AND BW1843U89 / Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: BL21 / Plasmid: PET17B / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P0A884, thymidylate synthase
#2: Chemical ChemComp-NDU / 2'-DEOXY-5-NITROURIDINE 5'-MONOPHOSPHATE


Type: DNA linking / Mass: 355.195 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H14N3O10P
#3: Chemical ChemComp-F89 / S)-2-(5(((1,2-DIHYDRO-3-METHYL-1-OXOBENZO(F)QUINAZOLIN-9-YL)METHYL)AMINO)1-OXO-2-ISOINDOLINYL)GLUTARIC ACID / FOLATE ANALOG 1843U89


Mass: 500.503 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H24N4O6
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, LYS 48 TO GLN ENGINEERED RESIDUE IN CHAIN B, LYS 48 TO GLN
Has protein modificationY
Nonpolymer details5-DIHYDROXYAMINO,2'-DEOXYURIDINE 5'-MONOPHOSPHATE (NDU): COVALENT LINK BETWEEN CYS 146 AND NDU 1265 ...5-DIHYDROXYAMINO,2'-DEOXYURIDINE 5'-MONOPHOSPHATE (NDU): COVALENT LINK BETWEEN CYS 146 AND NDU 1265 BETWEEN ATOMS SG AND C6.

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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: 2.6 Å3/Da / Density % sol: 54 % / Description: NONE
Crystal growpH: 7.5
Details: 20 MM POTASSIUM PHOSPHATE BUFFER, 4 MM DTT AND INCREMENTS IN AMMONIUM SULFATE FROM 2.05 TO 2.6 M, PH 7.5 TO 8

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.5418
DetectorType: ENRAF-NONIUS / Detector: AREA DETECTOR / Date: Nov 22, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→35.58 Å / Num. obs: 15793 / % possible obs: 95.1 % / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Rmerge(I) obs: 0.17 / Net I/σ(I): 3.7

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Processing

Software
NameVersionClassification
CNS1.2refinement
MADNESSdata reduction
PROCORdata reduction
Agrovatadata scaling
ROTAVATAdata scaling
SCALAdata scaling
TRUNCATEdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1FFL AND 1FWM

1ffl

1fwm


Resolution: 3→33.98 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 2316773.83 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Stereochemistry target values: MAXIMUM LIKELIHOOD TARGET USING AMPLITUDES
Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.239 611 5.1 %RANDOM
Rwork0.18 ---
obs0.18 12094 95.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 28.1663 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 20.1 Å2
Baniso -1Baniso -2Baniso -3
1--3.18 Å20 Å20 Å2
2---3.18 Å20 Å2
3---6.37 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.58 Å0.47 Å
Refinement stepCycle: LAST / Resolution: 3→33.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4306 0 125 29 4460
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
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_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.9
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.991.5
X-RAY DIFFRACTIONc_mcangle_it1.732
X-RAY DIFFRACTIONc_scbond_it1.452
X-RAY DIFFRACTIONc_scangle_it2.362.5
LS refinement shellResolution: 3→3.19 Å / Rfactor Rfree error: 0.037 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.35 91 4.8 %
Rwork0.282 1802 -
obs--89.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3U89.PARU89.TOP
X-RAY DIFFRACTION4LIGAND.PARLIGAND2.TOP
X-RAY DIFFRACTION5ION.PARAMION.TOP

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