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- PDB-5x69: Human thymidylate synthase with a fragment bound in the dimer int... -

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Basic information

Entry
Database: PDB / ID: 5x69
TitleHuman thymidylate synthase with a fragment bound in the dimer interface
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 / 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
Chem-7ZC / 2'-DEOXYURIDINE 5'-MONOPHOSPHATE / Thymidylate synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.69 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 21, 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)201,16612
Polymers199,5256
Non-polymers1,6416
Water1,42379
1
A: Thymidylate synthase
D: Thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,3295
Polymers66,5082
Non-polymers8213
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6010 Å2
ΔGint-31 kcal/mol
Surface area22140 Å2
MethodPISA
2
B: Thymidylate synthase
E: Thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,0214
Polymers66,5082
Non-polymers5122
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5020 Å2
ΔGint-27 kcal/mol
Surface area22350 Å2
MethodPISA
3
C: Thymidylate synthase
F: Thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,8163
Polymers66,5082
Non-polymers3081
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4950 Å2
ΔGint-27 kcal/mol
Surface area21910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.353, 109.353, 315.380
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: 0 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / Refine code: 0

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLUAA26 - 3103 - 287
21GLUGLUBB26 - 3103 - 287
12PROPROAA26 - 3053 - 282
22PROPROCC26 - 3053 - 282
13METMETAA26 - 3093 - 286
23METMETDD26 - 3093 - 286
14PROPROAA26 - 3053 - 282
24PROPROEE26 - 3053 - 282
15PROPROAA26 - 3053 - 282
25PROPROFF26 - 3053 - 282
16PROPROBB26 - 3053 - 282
26PROPROCC26 - 3053 - 282
17METMETBB26 - 3093 - 286
27METMETDD26 - 3093 - 286
18THRTHRBB26 - 3063 - 283
28THRTHREE26 - 3063 - 283
19PROPROBB26 - 3053 - 282
29PROPROFF26 - 3053 - 282
110THRTHRCC26 - 3063 - 283
210THRTHRDD26 - 3063 - 283
111THRTHRCC26 - 3063 - 283
211THRTHREE26 - 3063 - 283
112THRTHRCC26 - 3063 - 283
212THRTHRFF26 - 3063 - 283
113THRTHRDD26 - 3063 - 283
213THRTHREE26 - 3063 - 283
114PROPRODD26 - 3053 - 282
214PROPROFF26 - 3053 - 282
115THRTHREE26 - 3063 - 283
215THRTHRFF26 - 3063 - 283

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-7ZC / 1-(5-methoxy-1H-indol-3-yl)-N,N-dimethyl-methanamine


Mass: 204.268 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H16N2O
#3: Chemical
ChemComp-UMP / 2'-DEOXYURIDINE 5'-MONOPHOSPHATE / DUMP / Deoxyuridine monophosphate


Mass: 308.182 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H13N2O8P
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 79 / 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: 2.38 Å3/Da / Density % sol: 48.28 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 100mM sodium calcodylate, pH 6.5, 25% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 0.999999 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 14, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999999 Å / Relative weight: 1
ReflectionResolution: 2.69→30 Å / Num. obs: 53294 / % possible obs: 98.4 % / Redundancy: 10.7 % / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.036 / Rrim(I) all: 0.12 / Χ2: 1.16 / Net I/σ(I): 7.1 / Num. measured all: 569527
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.7-2.86.90.42948410.9350.1720.4650.38891.1
2.8-2.917.50.37550500.9560.1450.4030.45795.3
2.91-3.048.10.30553040.9740.1140.3270.56599.4
3.04-3.28.90.24652980.9840.0880.2620.73499.9
3.2-3.49.60.18753710.9920.0640.1981.009100
3.4-3.6611.50.14453660.9930.0460.1511.22399.9
3.66-4.0312.50.11453940.9960.0350.121.46100
4.03-4.6113.20.09554220.9970.0290.0991.62299.9
4.61-5.813.90.08855150.9980.0260.0921.594100
5.8-3013.80.06757330.9990.0190.0691.2898.7

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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: 2.69→22.175 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.939 / SU B: 13.342 / SU ML: 0.266 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.695 / ESU R Free: 0.352 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2455 2698 5.1 %RANDOM
Rwork0.2091 ---
obs0.211 50502 98.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 105.97 Å2 / Biso mean: 40.324 Å2 / Biso min: 16.57 Å2
Baniso -1Baniso -2Baniso -3
1-0.61 Å20 Å20 Å2
2--0.61 Å20 Å2
3----1.22 Å2
Refinement stepCycle: final / Resolution: 2.69→22.175 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13502 0 110 79 13691
Biso mean--70.67 29.11 -
Num. residues----1692
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01913980
X-RAY DIFFRACTIONr_bond_other_d0.0020.0213136
X-RAY DIFFRACTIONr_angle_refined_deg1.6391.96718949
X-RAY DIFFRACTIONr_angle_other_deg0.978330160
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2551684
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.80123.162661
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.418152307
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.26715109
X-RAY DIFFRACTIONr_chiral_restr0.0860.22004
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02115763
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023390
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A186160.05
12B186160.05
21A176800.06
22C176800.06
31A181720.06
32D181720.06
41A176840.07
42E176840.07
51A177640.06
52F177640.06
61B175660.07
62C175660.07
71B181040.07
72D181040.07
81B176380.07
82E176380.07
91B177320.07
92F177320.07
101C174720.07
102D174720.07
111C175300.07
112E175300.07
121C173260.07
122F173260.07
131D177160.06
132E177160.06
141D177540.06
142F177540.06
151E174620.07
152F174620.07
LS refinement shellResolution: 2.691→2.76 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 169 -
Rwork0.311 3338 -
all-3507 -
obs--89.1 %

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