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- PDB-5wrn: Human thymidylate synthase complexed with dCMP -

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Basic information

Entry
Database: PDB / ID: 5wrn
TitleHuman thymidylate synthase complexed with dCMP
ComponentsThymidylate synthase
KeywordsTRANSFERASE / Complex / nucleotide
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 / dihydrofolate reductase activity / response to glucocorticoid / mRNA regulatory element binding translation repressor activity / response to cytokine / response to progesterone / 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 / cytoplasm / cytosol
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
2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE / Thymidylate synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.39 Å
AuthorsChen, D. / Nordlund, P.
Funding support Singapore, 1items
OrganizationGrant numberCountry
Nanyang Technological UniversityM060080004.70301200 Singapore
CitationJournal: To Be Published
Title: Human thymidylate synthase complexed with dCMP
Authors: Almqvist, H. / Axelsson, H. / Jafari, R. / Chen, D. / Mateus, A. / Haraldsson, M. / Larsson, A. / Martinez Molina, D. / Artursson, P. / Lundback, T. / Nordlund, P.
History
DepositionDec 2, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 14, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low
Revision 2.0May 29, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / struct_site
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.pdbx_formal_charge / _atom_site.type_symbol / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.type / _chem_comp_atom.atom_id / _chem_comp_atom.comp_id / _chem_comp_atom.pdbx_stereo_config / _chem_comp_atom.type_symbol / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _chem_comp_bond.comp_id / _chem_comp_bond.value_order / _pdbx_entity_nonpoly.comp_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _struct_site.details / _struct_site.pdbx_auth_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Thymidylate synthase
A: Thymidylate synthase
C: Thymidylate synthase
D: Thymidylate synthase
E: Thymidylate synthase
F: Thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)200,84512
Polymers199,0026
Non-polymers1,8436
Water5,909328
1
B: Thymidylate synthase
A: Thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,9484
Polymers66,3342
Non-polymers6142
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4280 Å2
ΔGint-24 kcal/mol
Surface area22580 Å2
MethodPISA
2
C: Thymidylate synthase
D: Thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,9484
Polymers66,3342
Non-polymers6142
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4270 Å2
ΔGint-25 kcal/mol
Surface area22750 Å2
MethodPISA
3
E: Thymidylate synthase
F: Thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,9484
Polymers66,3342
Non-polymers6142
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4160 Å2
ΔGint-22 kcal/mol
Surface area22690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.096, 110.096, 317.268
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein
Thymidylate synthase / TSase


Mass: 33167.047 Da / Num. of mol.: 6 / Fragment: UNP residues 26-313
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-DCM / 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE


Mass: 307.197 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C9H14N3O7P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 328 / 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: 2.42 Å3/Da / Density % sol: 49.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 100 mM Sodium cacodylate 15% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1.000001 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Mar 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.000001 Å / Relative weight: 1
ReflectionResolution: 2.39→30 Å / Num. obs: 76815 / % possible obs: 98.4 % / Redundancy: 9.3 % / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.022 / Rrim(I) all: 0.071 / Χ2: 0.885 / Net I/σ(I): 13.3 / Num. measured all: 711815
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.39-2.438.50.31535830.9780.1020.3320.88294.2
2.43-2.488.50.28736330.9820.0930.3030.87594.9
2.48-2.528.50.26236750.9870.0850.2770.85995.3
2.52-2.578.40.24336890.9860.0790.2570.89696.1
2.57-2.638.40.21136960.9920.0690.2230.89896.2
2.63-2.698.40.19337510.9910.0630.2040.90797.3
2.69-2.768.50.16437660.9920.0540.1740.90697.9
2.76-2.838.50.14437900.9940.0470.1520.92498.3
2.83-2.928.70.1338150.9940.0430.1370.92498.9
2.92-3.018.80.1138350.9960.0360.1160.9299.4
3.01-3.128.90.09438590.9970.0310.0990.9399.4
3.12-3.249.20.08238970.9980.0270.0860.93899.9
3.24-3.399.60.06938670.9980.0220.0730.922100
3.39-3.579.80.06239060.9980.020.0660.935100
3.57-3.7910.20.05539150.9980.0170.0570.874100
3.79-4.0810.50.0539180.9990.0160.0530.874100
4.08-4.4910.60.05139340.9990.0160.0540.965100
4.49-5.1410.50.04939880.9990.0160.0511.03799.9
5.14-6.4710.30.04640550.9990.0140.0480.769100
6.47-30100.03142430.9990.010.0330.5399.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data collection
HKL-2000data scaling
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
PHASERphasing
HKLdata reduction
HKLdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HVY

1hvy


Resolution: 2.39→30 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.934 / SU B: 8.06 / SU ML: 0.186 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.427 / ESU R Free: 0.266 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2473 3757 4.9 %RANDOM
Rwork0.1876 ---
obs0.1906 72809 98.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 131.4 Å2 / Biso mean: 37.393 Å2 / Biso min: 15.09 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å20 Å20 Å2
2---0.17 Å20 Å2
3---0.34 Å2
Refinement stepCycle: final / Resolution: 2.39→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13656 0 120 328 14104
Biso mean--63.91 34.75 -
Num. residues----1697
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.01914149
X-RAY DIFFRACTIONr_bond_other_d0.0020.0213341
X-RAY DIFFRACTIONr_angle_refined_deg1.7661.97219164
X-RAY DIFFRACTIONr_angle_other_deg1.016330690
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.99151689
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.38923.299682
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.057152393
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.76915112
X-RAY DIFFRACTIONr_chiral_restr0.0950.22018
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02115897
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023399
LS refinement shellResolution: 2.391→2.453 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 272 -
Rwork0.222 4953 -
all-5225 -
obs--91.99 %

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