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- PDB-4g6w: Human Thymidylate Synthase M190K with bound 4-Bromobenzene-1,2,3-triol -

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Basic information

Entry
Database: PDB / ID: 4g6w
TitleHuman Thymidylate Synthase M190K with bound 4-Bromobenzene-1,2,3-triol
ComponentsThymidylate synthase
KeywordsTRANSFERASE / Methyltransferase
Function / homology
Function and homology information


uracil metabolic process / response to organophosphorus / intestinal epithelial cell maturation / Interconversion of nucleotide di- and triphosphates / response to folic acid / thymidylate synthase / sequence-specific mRNA binding / cartilage development / response to vitamin A / tetrahydrofolate interconversion ...uracil metabolic process / response to organophosphorus / intestinal epithelial cell maturation / Interconversion of nucleotide di- and triphosphates / response to folic acid / thymidylate synthase / sequence-specific mRNA binding / cartilage development / response to vitamin A / tetrahydrofolate interconversion / thymidylate synthase activity / folic acid binding / dTMP biosynthetic process / dTTP biosynthetic process / DNA biosynthetic process / G1/S-Specific Transcription / developmental growth / response to glucocorticoid / response to cytokine / mRNA regulatory element binding translation repressor activity / liver regeneration / response to progesterone / response to toxic substance / circadian rhythm / response to ethanol / methylation / mitochondrial inner membrane / negative regulation of translation / mitochondrial matrix / response to xenobiotic stimulus / protein homodimerization activity / mitochondrion / nucleus / cytosol / cytoplasm
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
4-bromobenzene-1,2,3-triol / Thymidylate synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsCeleste, L.R. / Lebioda, L.
CitationJournal: To be Published / Year: 2012
Title: Oxidation of Cysteine 195 of Huyman Thymidylate Synthase by Purpurogallin
Authors: Celeste, L.R. / Lovelace, L.L. / Lebioda, L.
History
DepositionJul 19, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 19, 2014Group: Structure summary
Revision 1.2Sep 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 / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
X: Thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2664
Polymers35,8691
Non-polymers3973
Water1,20767
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
X: Thymidylate synthase
hetero molecules

X: Thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,5328
Polymers71,7382
Non-polymers7946
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+2/31
Buried area4070 Å2
ΔGint-14 kcal/mol
Surface area23300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.846, 95.846, 80.525
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11X-600-

PBX

21X-600-

PBX

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Components

#1: Protein Thymidylate synthase


Mass: 35869.035 Da / Num. of mol.: 1 / Mutation: M190K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: tyms, ts, ok/sw-cl.29 / Plasmid: pTSO80 / Production host: Escherichia coli (E. coli) / Strain (production host): TX61- / References: UniProt: P04818, thymidylate synthase
#2: Chemical ChemComp-PBX / 4-bromobenzene-1,2,3-triol


Mass: 205.006 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5BrO3
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.01 Å3/Da / Density % sol: 59.13 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 100 mM Tris pH 7.5-8.5, 20 mM BME, 25-42% Ammonium Sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 278K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 3, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 19433 / Num. obs: 19433 / % possible obs: 94.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 6.4 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 15.2
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.422 / % possible all: 94.1

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3EHI

3ehi


Resolution: 2.3→50 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.922 / WRfactor Rfree: 0.262 / WRfactor Rwork: 0.2251 / Occupancy max: 1 / Occupancy min: 0.25 / FOM work R set: 0.8034 / SU B: 0.006 / SU ML: 0 / SU R Cruickshank DPI: 0.1891 / SU Rfree: 0.2249 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.189 / ESU R Free: 0.225 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2635 933 5.1 %RANDOM
Rwork0.2215 ---
all0.2236 19429 --
obs0.2236 18295 94.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 97.03 Å2 / Biso mean: 48.2932 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1--1.79 Å2-0.89 Å20 Å2
2---1.79 Å20 Å2
3---2.68 Å2
Refinement stepCycle: LAST / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2135 0 20 67 2222
LS refinement shellResolution: 2.298→2.358 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 70 -
Rwork0.282 1261 -
all-1331 -
obs--94.26 %

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