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- PDB-4h1i: Structure of human thymidylate synthase at low salt conditions -

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Basic information

Entry
Database: PDB / ID: 4h1i
TitleStructure of human thymidylate synthase at low salt conditions
ComponentsThymidylate synthase
KeywordsTRANSFERASE / nucleotide metabolism / cancer chemotherapy target / 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 / G1/S-Specific Transcription / DNA biosynthetic process / developmental growth / 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: 3.095 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 10, 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
B: Thymidylate synthase
C: Thymidylate synthase
D: Thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,1998
Polymers145,8154
Non-polymers3844
Water37821
1
A: Thymidylate synthase
C: Thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,0994
Polymers72,9072
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5160 Å2
ΔGint-56 kcal/mol
Surface area22610 Å2
MethodPISA
2
B: Thymidylate synthase
D: Thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,0994
Polymers72,9072
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5100 Å2
ΔGint-56 kcal/mol
Surface area22910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)157.855, 94.927, 131.439
Angle α, β, γ (deg.)90.00, 122.75, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Thymidylate synthase / / TS / TSase


Mass: 36453.664 Da / Num. of mol.: 4
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.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 2.84 Å3/Da / Density % sol: 61.71 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Protein at 5mg/ml, 30% PEG 1500, 15mM ammonium sulfate, 20mM 2-mercaptoethanol, 3% w/v 1,5-Diaminopentane dihydrochloride, pH 8.0, 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: May 8, 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: 3.1→19.9 Å / Num. all: 29851 / Num. obs: 29732 / % possible obs: 99.6 % / Observed criterion σ(F): 1.34 / Observed criterion σ(I): 1.34 / Redundancy: 6.2 % / Net I/σ(I): 8.6
Reflection shellResolution: 3.1→3.2 Å / Redundancy: 5.2 % / Mean I/σ(I) obs: 2.05 / % possible all: 98.6

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HW4

1hw4


Resolution: 3.095→19.888 Å / SU ML: 0.46 / σ(F): 1.34 / Phase error: 28.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2849 1507 5.07 %RANDOM
Rwork0.2317 ---
obs0.2344 29732 99.6 %-
all-29851 --
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 16.177 Å2 / ksol: 0.297 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--5.8616 Å20 Å2-1.2716 Å2
2--6.6666 Å2-0 Å2
3---5.8914 Å2
Refinement stepCycle: LAST / Resolution: 3.095→19.888 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9080 0 20 21 9121
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0039336
X-RAY DIFFRACTIONf_angle_d0.7712636
X-RAY DIFFRACTIONf_dihedral_angle_d14.3063496
X-RAY DIFFRACTIONf_chiral_restr0.0561324
X-RAY DIFFRACTIONf_plane_restr0.0041644
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0954-3.19490.36151150.33192513X-RAY DIFFRACTION97
3.1949-3.30860.37041490.28322540X-RAY DIFFRACTION100
3.3086-3.44040.32291260.26252577X-RAY DIFFRACTION100
3.4404-3.59610.28661350.23222554X-RAY DIFFRACTION100
3.5961-3.78450.27521380.22082577X-RAY DIFFRACTION100
3.7845-4.01970.30571340.22512570X-RAY DIFFRACTION100
4.0197-4.32720.23361350.20132541X-RAY DIFFRACTION100
4.3272-4.75720.22841460.19122580X-RAY DIFFRACTION100
4.7572-5.43330.30981570.21282569X-RAY DIFFRACTION100
5.4333-6.79960.30071420.25522582X-RAY DIFFRACTION100
6.7996-19.88830.26671300.23492622X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -72.4289 Å / Origin y: -31.8985 Å / Origin z: 144.0364 Å
111213212223313233
T-0.1718 Å2-0.2439 Å2-0.05 Å2--0.1244 Å2-0.1216 Å2--0.0603 Å2
L0.5503 °20.3279 °2-0.0455 °2-0.2779 °2-0.0565 °2--0.0576 °2
S-0.2337 Å °0.0118 Å °0.0067 Å °-0.0562 Å °0.1651 Å °-0.0388 Å °-0.0285 Å °0.0384 Å °-0.0666 Å °
Refinement TLS groupSelection details: all

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