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- PDB-4gyh: Structure of human thymidylate synthase at high salt conditions -

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Basic information

Entry
Database: PDB / ID: 4gyh
TitleStructure of human thymidylate synthase at high salt conditions
ComponentsThymidylate synthase
KeywordsTRANSFERASE / Methyl transferase
Function / homology
Function and homology information


uracil metabolic process / response to organophosphorus / intestinal epithelial cell maturation / response to folic acid / Interconversion of nucleotide di- and triphosphates / response to vitamin A / thymidylate synthase / sequence-specific mRNA binding / cartilage development / tetrahydrofolate interconversion ...uracil metabolic process / response to organophosphorus / intestinal epithelial cell maturation / response to folic acid / Interconversion of nucleotide di- and triphosphates / response to vitamin A / thymidylate synthase / sequence-specific mRNA binding / cartilage development / tetrahydrofolate interconversion / thymidylate synthase activity / folic acid binding / dTMP biosynthetic process / dTTP biosynthetic process / DNA biosynthetic process / G1/S-Specific Transcription / developmental growth / dihydrofolate reductase activity / response to glucocorticoid / mRNA regulatory element binding translation repressor activity / response to progesterone / response to cytokine / liver regeneration / response to toxic substance / circadian rhythm / methylation / response to ethanol / 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/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
Thymidylate synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.005 Å
AuthorsBrunn, N. / Dibrov, S. / Hermann, T.
CitationJournal: Biosci.Rep. / Year: 2014
Title: Analysis of mRNA recognition by human thymidylate synthase.
Authors: Brunn, N.D. / Dibrov, S.M. / Kao, M.B. / Ghassemian, M. / Hermann, T.
History
DepositionSep 5, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2014Group: Database references
Revision 1.2Jan 28, 2015Group: Database references
Revision 1.3Sep 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_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

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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)36,6463
Polymers36,4541
Non-polymers1922
Water0
1
A: Thymidylate synthase
hetero molecules

A: Thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,2926
Polymers72,9072
Non-polymers3844
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+2/31
Buried area4720 Å2
ΔGint-69 kcal/mol
Surface area22110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.194, 96.194, 83.275
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Thymidylate synthase / / TS / TSase


Mass: 36453.664 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TYMS, TS, OK/SW-cl.29 / Production host: Escherichia coli (E. coli) / References: UniProt: P04818, thymidylate synthase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4

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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: 3.05 Å3/Da / Density % sol: 59.69 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 100mM TRIS, 1.8M Ammonium Sulfate, 20mM 2-mercaptoethanol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Oct 26, 2011
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3→19.6 Å / Num. all: 9141 / Num. obs: 8628 / % possible obs: 94.4 % / Observed criterion σ(F): 1.35 / Observed criterion σ(I): 1.35 / Redundancy: 7.9 % / Net I/σ(I): 11
Reflection shellResolution: 3→3.1 Å / % possible all: 97.6

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HW4

1hw4


Resolution: 3.005→19.632 Å / SU ML: 0.97 / σ(F): 1.34 / Phase error: 28.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2802 869 10.07 %RANDOM
Rwork0.215 ---
obs0.2216 8628 94.39 %-
all-10060 --
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.315 Å2 / ksol: 0.35 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--5.3941 Å20 Å20 Å2
2---5.3941 Å2-0 Å2
3---10.7883 Å2
Refinement stepCycle: LAST / Resolution: 3.005→19.632 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2125 0 10 0 2135
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092188
X-RAY DIFFRACTIONf_angle_d1.2122960
X-RAY DIFFRACTIONf_dihedral_angle_d20.137823
X-RAY DIFFRACTIONf_chiral_restr0.075312
X-RAY DIFFRACTIONf_plane_restr0.004382
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.005-3.19250.41211390.31911278X-RAY DIFFRACTION95
3.1925-3.43780.30151560.2381357X-RAY DIFFRACTION100
3.4378-3.78150.45891070.316950X-RAY DIFFRACTION72
3.7815-4.32360.27041530.21461358X-RAY DIFFRACTION99
4.3236-5.42820.22071580.16081369X-RAY DIFFRACTION100
5.4282-19.63220.22511560.18541447X-RAY DIFFRACTION100

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