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- PDB-5x4x: Mutant human thymidylate synthase A191K crystallized in a sulfate... -

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Basic information

Entry
Database: PDB / ID: 5x4x
TitleMutant human thymidylate synthase A191K crystallized in a sulfate-containing condition
ComponentsThymidylate synthase
KeywordsTRANSFERASE / methyltransferase
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 / thymidylate synthase / response to vitamin A / 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 / thymidylate synthase / response to vitamin A / 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 / response to glucocorticoid / mRNA regulatory element binding translation repressor activity / response to cytokine / response to progesterone / liver regeneration / 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
Thymidylate synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 Å
AuthorsChen, D. / Jansson, A. / Larsson, A. / Nordlund, P.
Funding support Singapore, 1items
OrganizationGrant numberCountry
Nanyang Technological UniversityM060080004.70301200 Singapore
CitationJournal: J. Biol. Chem. / Year: 2017
Title: Structural analyses of human thymidylate synthase reveal a site that may control conformational switching between active and inactive states
Authors: Chen, D. / Jansson, A. / Sim, D. / Larsson, A. / Nordlund, P.
History
DepositionFeb 14, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 28, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2017Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)36,1003
Polymers35,9081
Non-polymers1922
Water1,35175
1
A: Thymidylate synthase
hetero molecules

A: Thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,2006
Polymers71,8162
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-2/31
Buried area4890 Å2
ΔGint-79 kcal/mol
Surface area23390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.460, 95.460, 81.181
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Thymidylate synthase / TSase


Mass: 35908.113 Da / Num. of mol.: 1 / Mutation: A191K
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


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


Mass: 18.015 Da / Num. of mol.: 75 / 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: 3.26 Å3/Da / Density % sol: 62.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 100mM Tris, pH 8.5, 0.2M lithium sulfate, 1.26M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 7, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.314→82.671 Å / Num. all: 19057 / Num. obs: 19057 / % possible obs: 100 % / Redundancy: 10.6 % / Rpim(I) all: 0.022 / Rrim(I) all: 0.073 / Rsym value: 0.07 / Net I/av σ(I): 8.4 / Net I/σ(I): 22.1 / Num. measured all: 201463
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
2.31-2.4410.20.292.72808327590.0950.3050.297.4100
2.44-2.5910.80.2233.52807025910.0710.2340.2239.7100
2.59-2.7710.80.1624.72644124410.0520.170.16212.8100
2.77-2.9910.80.1146.52472422870.0360.1190.11417.4100
2.99-3.2710.80.0868.22265121020.0270.090.08622.9100
3.27-3.6610.70.06310.42057019190.020.0660.06331.1100
3.66-4.2210.60.05212.21800916960.0170.0540.05237.9100
4.22-5.1710.50.044141517214500.0140.0460.04443.9100
5.17-7.3210.20.05511.21176911540.0180.0570.05536.6100
7.32-29.1619.10.0341759746580.0120.0360.03440.998.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
SCALA3.3.22data scaling
PDB_EXTRACT3.22data extraction
MOSFLMdata processing
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HW3

1hw3


Resolution: 2.31→82.67 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.928 / SU B: 5.516 / SU ML: 0.133 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.208 / ESU R Free: 0.191 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2267 939 4.9 %RANDOM
Rwork0.1726 ---
obs0.1753 18074 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 105.5 Å2 / Biso mean: 39.021 Å2 / Biso min: 16.91 Å2
Baniso -1Baniso -2Baniso -3
1--1.76 Å2-0.88 Å20 Å2
2---1.76 Å20 Å2
3---5.72 Å2
Refinement stepCycle: final / Resolution: 2.31→82.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2208 0 10 75 2293
Biso mean--39.87 36.38 -
Num. residues----275
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0192296
X-RAY DIFFRACTIONr_bond_other_d0.0020.022152
X-RAY DIFFRACTIONr_angle_refined_deg1.851.9653109
X-RAY DIFFRACTIONr_angle_other_deg1.0434943
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1765277
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.92323.304112
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.76415387
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3751518
X-RAY DIFFRACTIONr_chiral_restr0.1210.2331
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212593
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02555
LS refinement shellResolution: 2.314→2.374 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.378 76 -
Rwork0.233 1300 -
all-1376 -
obs--100 %

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