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- PDB-5x4w: Mutant human thymidylate synthase A191K crystallized in a sulfate... -

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Basic information

Entry
Database: PDB / ID: 5x4w
TitleMutant human thymidylate synthase A191K crystallized in a sulfate-free condition
ComponentsThymidylate synthase
KeywordsTRANSFERASE / methyltransferase
Function / homology
Function and homology information


Interconversion of nucleotide di- and triphosphates / thymidylate synthase / sequence-specific mRNA binding / folic acid binding / tetrahydrofolate interconversion / thymidylate synthase activity / dTMP biosynthetic process / dTTP biosynthetic process / DNA biosynthetic process / G1/S-Specific Transcription ...Interconversion of nucleotide di- and triphosphates / thymidylate synthase / sequence-specific mRNA binding / folic acid binding / tetrahydrofolate interconversion / thymidylate synthase activity / dTMP biosynthetic process / dTTP biosynthetic process / DNA biosynthetic process / G1/S-Specific Transcription / mRNA regulatory element binding translation repressor activity / methylation / mitochondrial inner membrane / negative regulation of translation / mitochondrial matrix / mitochondrion / nucleus / cytoplasm / 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
PHOSPHATE ION / Thymidylate synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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)36,0983
Polymers35,9081
Non-polymers1902
Water2,414134
1
A: Thymidylate synthase
hetero molecules

A: Thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,1966
Polymers71,8162
Non-polymers3804
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-2/31
Buried area5060 Å2
ΔGint-42 kcal/mol
Surface area23260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.590, 95.590, 79.671
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-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / 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: 3.19 Å3/Da / Density % sol: 61.46 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 100mM HEPES, pH 7.0, 10% PEG 6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / 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: 2.1→82.783 Å / Num. all: 24955 / Num. obs: 24955 / % possible obs: 99.9 % / Redundancy: 10.2 % / Rpim(I) all: 0.034 / Rrim(I) all: 0.108 / Rsym value: 0.102 / Net I/av σ(I): 4.7 / Net I/σ(I): 15 / Num. measured all: 254681
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
2.1-2.2110.50.35723817136280.1150.3750.3576.4100
2.21-2.3510.50.262.83573933990.0840.2730.268.1100
2.35-2.5110.50.1953.83355032060.0630.2050.19510.2100
2.51-2.7110.40.1534.73103529820.050.1610.15312.4100
2.71-2.9710.30.1156.12861127730.0370.1210.11515.9100
2.97-3.3210.20.0926.92547625000.030.0970.09219.5100
3.32-3.839.90.0827.32221622330.0270.0860.08223.6100
3.83-4.79.60.0787.51816918890.0270.0830.07826.4100
4.7-6.6490.086.91345414910.0280.0850.0824.299.3
6.64-30.69.70.0737.482608540.0250.0770.07326.598.8

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Processing

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

1hw3


Resolution: 2.1→82.78 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.954 / SU B: 3.292 / SU ML: 0.086 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.138 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1876 1285 5.2 %RANDOM
Rwork0.1569 ---
obs0.1585 23648 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 123.02 Å2 / Biso mean: 32.789 Å2 / Biso min: 14.18 Å2
Baniso -1Baniso -2Baniso -3
1--1.08 Å2-0.54 Å20 Å2
2---1.08 Å20 Å2
3---3.51 Å2
Refinement stepCycle: final / Resolution: 2.1→82.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2214 0 10 134 2358
Biso mean--35.69 40.28 -
Num. residues----276
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0192300
X-RAY DIFFRACTIONr_bond_other_d0.0020.022145
X-RAY DIFFRACTIONr_angle_refined_deg2.0411.9653116
X-RAY DIFFRACTIONr_angle_other_deg1.08834931
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.715277
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.53923.363113
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.65615384
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1581518
X-RAY DIFFRACTIONr_chiral_restr0.1240.2328
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212598
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02554
LS refinement shellResolution: 2.1→2.155 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 118 -
Rwork0.19 1732 -
all-1850 -
obs--100 %

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