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- PDB-5x5d: Human thymidylate synthase bound with dUMP -

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Basic information

Entry
Database: PDB / ID: 5x5d
TitleHuman thymidylate synthase bound with dUMP
ComponentsThymidylate synthase
KeywordsTRANSFERASE / methyltransferase
Function / homology
Function and homology information


thymidylate synthase / Interconversion of nucleotide di- and triphosphates / sequence-specific mRNA binding / folic acid binding / thymidylate synthase activity / tetrahydrofolate interconversion / dTMP biosynthetic process / dTTP biosynthetic process / DNA biosynthetic process / G1/S-Specific Transcription ...thymidylate synthase / Interconversion of nucleotide di- and triphosphates / sequence-specific mRNA binding / folic acid binding / thymidylate synthase activity / tetrahydrofolate interconversion / dTMP biosynthetic process / dTTP biosynthetic process / DNA biosynthetic process / G1/S-Specific Transcription / mRNA regulatory element binding translation repressor activity / methylation / negative regulation of translation / mitochondrial inner membrane / 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
2'-DEOXYURIDINE 5'-MONOPHOSPHATE / Thymidylate synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 15, 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 / refine_hist / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)201,37412
Polymers199,5256
Non-polymers1,8496
Water29,2561624
1
A: Thymidylate synthase
D: Thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,1254
Polymers66,5082
Non-polymers6162
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5510 Å2
ΔGint-31 kcal/mol
Surface area22280 Å2
MethodPISA
2
B: Thymidylate synthase
E: Thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,1254
Polymers66,5082
Non-polymers6162
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5440 Å2
ΔGint-30 kcal/mol
Surface area22590 Å2
MethodPISA
3
C: Thymidylate synthase
F: Thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,1254
Polymers66,5082
Non-polymers6162
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5620 Å2
ΔGint-33 kcal/mol
Surface area21980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.742, 109.742, 317.690
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16B
26C
17B
27D
18B
28E
19B
29F
110C
210D
111C
211E
112C
212F
113D
213E
114D
214F
115E
215F

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11VALVALAA26 - 3133 - 290
21VALVALBB26 - 3133 - 290
12GLUGLUAA26 - 3103 - 287
22GLUGLUCC26 - 3103 - 287
13METMETAA26 - 3093 - 286
23METMETDD26 - 3093 - 286
14PROPROAA26 - 3053 - 282
24PROPROEE26 - 3053 - 282
15LYSLYSAA26 - 3083 - 285
25LYSLYSFF26 - 3083 - 285
16GLUGLUBB26 - 3103 - 287
26GLUGLUCC26 - 3103 - 287
17METMETBB26 - 3093 - 286
27METMETDD26 - 3093 - 286
18PROPROBB26 - 3053 - 282
28PROPROEE26 - 3053 - 282
19LYSLYSBB26 - 3083 - 285
29LYSLYSFF26 - 3083 - 285
110METMETCC26 - 3093 - 286
210METMETDD26 - 3093 - 286
111PROPROCC26 - 3053 - 282
211PROPROEE26 - 3053 - 282
112LYSLYSCC26 - 3083 - 285
212LYSLYSFF26 - 3083 - 285
113PROPRODD26 - 3053 - 282
213PROPROEE26 - 3053 - 282
114LYSLYSDD26 - 3083 - 285
214LYSLYSFF26 - 3083 - 285
115PROPROEE26 - 3053 - 282
215PROPROFF26 - 3053 - 282

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

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Components

#1: Protein
Thymidylate synthase / TSase


Mass: 33254.125 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-UMP / 2'-DEOXYURIDINE 5'-MONOPHOSPHATE / DUMP


Mass: 308.182 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C9H13N2O8P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1624 / 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: 2.41 Å3/Da / Density % sol: 49.02 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 100mM sodium calcodylate, pH 6.5, 25% PEG 4000

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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 27, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 116562 / % possible obs: 88.2 % / Redundancy: 4 % / Rmerge(I) obs: 0.083 / Χ2: 1.042 / Net I/σ(I): 8.5 / Num. measured all: 463678
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2-2.074.90.403123551.013195.2
2.07-2.154.60.294123161.048194.3
2.15-2.254.40.224120631.059192.6
2.25-2.374.10.168118951.076191.2
2.37-2.523.80.133115541.079188.2
2.52-2.713.40.106111981.081185.2
2.71-2.9930.078108321.127182.1
2.99-3.422.50.051108301.241181.7
3.42-4.312.40.041112001.099183.6
4.31-306.30.041123190.905188.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
SCALEPACKdata scaling
PDB_EXTRACT3.22data extraction
HKL-2000data processing
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1I00

1i00


Resolution: 2→22.572 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.944 / SU B: 3.978 / SU ML: 0.109 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.189 / ESU R Free: 0.177 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2228 5830 5 %RANDOM
Rwork0.1808 ---
obs0.1829 110666 88.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 105.71 Å2 / Biso mean: 26.758 Å2 / Biso min: 9.52 Å2
Baniso -1Baniso -2Baniso -3
1-0.48 Å20 Å20 Å2
2--0.48 Å20 Å2
3----0.95 Å2
Refinement stepCycle: final / Resolution: 2→22.572 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13758 0 120 1624 15502
Biso mean--28.11 34.83 -
Num. residues----1712
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.01914268
X-RAY DIFFRACTIONr_angle_refined_deg1.8851.9719328
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.45251710
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.88323.358688
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.205152412
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.90315112
X-RAY DIFFRACTIONr_chiral_restr0.1260.22037
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02110944
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A192780.06
12B192780.06
21A190220.06
22C190220.06
31A187700.06
32D187700.06
41A184520.07
42E184520.07
51A184640.08
52F184640.08
61B189080.06
62C189080.06
71B187700.06
72D187700.06
81B183100.07
82E183100.07
91B185080.07
92F185080.07
101C187260.06
102D187260.06
111C183860.07
112E183860.07
121C184660.07
122F184660.07
131D185340.06
132E185340.06
141D187060.06
142F187060.06
151E183600.06
152F183600.06
LS refinement shellResolution: 1.997→2.049 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 423 -
Rwork0.235 8599 -
all-9022 -
obs--93.97 %

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