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- PDB-6k7q: Crystal structure of thymidylate synthase from shrimp -

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Basic information

Entry
Database: PDB / ID: 6k7q
TitleCrystal structure of thymidylate synthase from shrimp
ComponentsThymidylate synthase
KeywordsTRANSFERASE / thymidylate synthase / dUMP / dTMP / shrimp
Function / homology
Function and homology information


thymidylate synthase / thymidylate synthase activity / dTMP biosynthetic process / dTTP biosynthetic process / dihydrofolate reductase activity / methylation / mitochondrion / 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
Thymidylate synthase / Thymidylate synthase
Similarity search - Component
Biological speciesPenaeus vannamei (Pacific white shrimp)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 Å
AuthorsMa, Q. / Zang, K. / Liu, C.
Funding support China, 4items
OrganizationGrant numberCountry
Other government1000 talent program China
Chinese Academy of Sciences100 talent program China
National Natural Science Foundation of China China
National Natural Science Foundation of China China
CitationJournal: J Oceanol Limnol / Year: 2020
Title: Structural analysis of a shrimp thymidylate synthase reveals species-specific interactions with dUMP and raltitrexed.
Authors: Liu, C. / Zang, K. / Li, S. / Li, F. / Ma, Q.
History
DepositionJun 8, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 10, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 30, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.country / _citation.journal_id_ISSN ..._citation.country / _citation.journal_id_ISSN / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
G: Thymidylate synthase
H: Thymidylate synthase
I: Thymidylate synthase
J: Thymidylate synthase
K: Thymidylate synthase
L: Thymidylate synthase
M: Thymidylate synthase
N: Thymidylate synthase
O: Thymidylate synthase
P: Thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)541,30434
Polymers539,57516
Non-polymers1,72918
Water14,862825
1
A: Thymidylate synthase
B: Thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,6394
Polymers67,4472
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4400 Å2
ΔGint-57 kcal/mol
Surface area21550 Å2
MethodPISA
2
C: Thymidylate synthase
D: Thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,7355
Polymers67,4472
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4550 Å2
ΔGint-65 kcal/mol
Surface area21890 Å2
MethodPISA
3
E: Thymidylate synthase
F: Thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,6394
Polymers67,4472
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4410 Å2
ΔGint-58 kcal/mol
Surface area20960 Å2
MethodPISA
4
G: Thymidylate synthase
H: Thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,6394
Polymers67,4472
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4400 Å2
ΔGint-56 kcal/mol
Surface area21330 Å2
MethodPISA
5
I: Thymidylate synthase
J: Thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,7355
Polymers67,4472
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4410 Å2
ΔGint-58 kcal/mol
Surface area21650 Å2
MethodPISA
6
K: Thymidylate synthase
L: Thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,6394
Polymers67,4472
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4240 Å2
ΔGint-58 kcal/mol
Surface area20970 Å2
MethodPISA
7
M: Thymidylate synthase
N: Thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,6394
Polymers67,4472
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4410 Å2
ΔGint-58 kcal/mol
Surface area21070 Å2
MethodPISA
8
O: Thymidylate synthase
P: Thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,6394
Polymers67,4472
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4410 Å2
ΔGint-69 kcal/mol
Surface area21330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.270, 103.458, 125.768
Angle α, β, γ (deg.)77.40, 84.81, 61.43
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Thymidylate synthase


Mass: 33723.430 Da / Num. of mol.: 16
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Penaeus vannamei (Pacific white shrimp)
Gene: TS / Production host: Escherichia coli (E. coli)
References: UniProt: C6GJB8, UniProt: A0A423U5Z1*PLUS, thymidylate synthase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 825 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.13 Å3/Da / Density % sol: 42.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 1 ul protein solution (20 mg/ml in 10 mM HEPES, 150 mM NaCl, 1 mM DTT, pH 7.5) and 1 ul reservoir solution containing 18% (w/v) PEG 3350, 200 mM (NH4)2SO4, 100 mM HEPES, pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97931 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 4, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 2.269→122.723 Å / Num. obs: 200394 / % possible obs: 97.1 % / Redundancy: 2 % / Biso Wilson estimate: 40.11 Å2 / CC1/2: 0.99 / Rpim(I) all: 0.054 / Rrim(I) all: 0.076 / Rsym value: 0.054 / Net I/σ(I): 9.3
Reflection shellResolution: 2.269→2.277 Å / Redundancy: 2 % / Mean I/σ(I) obs: 2.8 / Num. unique obs: 1671 / CC1/2: 0.91 / Rpim(I) all: 0.276 / Rrim(I) all: 0.391 / Rsym value: 0.277 / % possible all: 80.1

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSJan 26, 2018, built on 20180409data reduction
Aimlessversion 0.5.29data scaling
PHASER2.7.17phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HVY

1hvy


Resolution: 2.27→89.03 Å / Cor.coef. Fo:Fc: 0.903 / Cor.coef. Fo:Fc free: 0.908 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.392 / Cross valid method: FREE R-VALUE / σ(F): 0 / SU R Blow DPI: 0.362 / SU Rfree Blow DPI: 0.22 / SU Rfree Cruickshank DPI: 0.228
RfactorNum. reflection% reflectionSelection details
Rfree0.236 10707 5.39 %thin shells
Rwork0.218 ---
obs0.219 198472 96.2 %-
Displacement parametersBiso mean: 40.68 Å2
Baniso -1Baniso -2Baniso -3
1--4.4724 Å26.1223 Å2-0.7791 Å2
2--0.7059 Å2-0.2059 Å2
3---3.7664 Å2
Refine analyzeLuzzati coordinate error obs: 0.36 Å
Refinement stepCycle: 1 / Resolution: 2.27→89.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms34386 0 90 825 35301
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0135378HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.147842HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d12274SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes919HARMONIC2
X-RAY DIFFRACTIONt_gen_planes5074HARMONIC5
X-RAY DIFFRACTIONt_it35378HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.96
X-RAY DIFFRACTIONt_other_torsion19.54
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion4337SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact38723SEMIHARMONIC4
LS refinement shellResolution: 2.27→2.33 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 1589 12.5 %
Rwork0.248 11128 -
all0.253 12717 -
obs--83.26 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.09260.20510.92951.1614-0.27842.5759-0.094-0.0347-0.1001-0.3010.15210.07310.0619-0.2471-0.0580.025-0.0533-0.0047-0.1761-0.0234-0.207419.8694-50.8808-42.3419
20.62570.63360.62341.95580.60193.21260.118-0.1240.00820.2978-0.22640.0990.08560.01880.1083-0.0161-0.0972-0.0328-0.1196-0.0051-0.28738.24368.596244.6334
30.96340.9089-0.03772.21050.65192.15650.1173-0.1395-0.03180.3429-0.161-0.09360.10490.32870.0437-0.0036-0.0426-0.0281-0.07540.0335-0.2941-47.4369-4.4119-17.2593
41.09420.65070.95311.86150.71122.5783-0.14110.09320.1053-0.2066-0.02170.1645-0.1273-0.06680.1628-0.0405-0.0125-0.0603-0.1266-0.0332-0.2317-0.85895.937817.8806
50.58010.4344-0.01011.46430.14082.991-0.10950.09230.01-0.17660.05560.10880.09530.06910.054-0.0108-0.0618-0.0168-0.12950.0019-0.2236-57.5383-5.2644-43.8176
60.79410.7123-0.16772.1141-1.11093.2978-0.18340.2137-0.0002-0.28490.25040.11610.3181-0.4038-0.06690.0003-0.1794-0.0392-0.1373-0.0737-0.295-25.439-38.806716.8135
70.87580.7238-0.60591.6494-1.35483.71870.1769-0.0987-0.0770.4485-0.3989-0.239-0.21930.39440.22210.0064-0.1954-0.0662-0.1364-0.0113-0.3044-15.5542-37.034243.1738
81.0560.6147-0.19841.92751.6765.807-0.33050.1403-0.1278-0.28310.0403-0.12350.50740.03980.29020.0513-0.1740.079-0.194-0.0433-0.3441-0.8153-12.9398-42.9918
91.39630.3844-0.43611.6230.1994.1072-0.0658-0.04730.02210.1212-0.12860.0327-0.081-0.02990.1944-0.011-0.1282-0.0041-0.1083-0.0663-0.3161-4.8746-3.3083-16.6885
101.40390.5228-0.5981.72170.4833.4505-0.33520.1002-0.2704-0.36970.0211-0.09170.079-0.11690.3142-0.0015-0.12120.0357-0.202-0.094-0.2499-25.6432-58.2069-43.8258
111.00640.6973-0.25441.27060.20652.49680.1731-0.14570.03720.1653-0.1925-0.0175-0.1761-0.02760.0194-0.1004-0.0896-0.0027-0.0624-0.1165-0.1906-29.3112-47.9856-17.7487
120.50420.13620.15971.2140.15533.2286-0.09170.0737-0.0425-0.34460.0978-0.08970.29090.3208-0.00610.0559-0.03320.0179-0.1644-0.0353-0.270532.9279-44.927919.5825
130.49590.3190.06430.9208-0.01552.44150.0346-0.01170.00180.1656-0.05660.0763-0.02370.04520.0219-0.0252-0.03980.015-0.1155-0.0266-0.155628.2016-35.684246.0085
141.36560.8713-0.48731.09890.22614.6653-0.16370.2515-0.0735-0.21260.0445-0.12160.1855-0.64170.1192-0.1213-0.03610.0394-0.0623-0.0267-0.3179-46.12310.440618.2267
151.47090.1558-1.42261.1561.07343.60240.28960.01390.18140.1439-0.2069-0.0023-0.3107-0.5136-0.0828-0.0489-0.07380.003-0.1091-0.0196-0.3007-51.271311.032744.1711
160.58610.51870.44781.5532-0.06212.96320.0516-0.0777-0.02240.3506-0.1391-0.1069-0.0499-0.1040.0874-0.0494-0.0217-0.0445-0.13480.0106-0.201730.1781-48.6754-15.9957
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ N|* }
2X-RAY DIFFRACTION2{ A|* }
3X-RAY DIFFRACTION3{ O|* }
4X-RAY DIFFRACTION4{ B|* }
5X-RAY DIFFRACTION5{ P|* }
6X-RAY DIFFRACTION6{ C|* }
7X-RAY DIFFRACTION7{ D|* }
8X-RAY DIFFRACTION8{ E|* }
9X-RAY DIFFRACTION9{ F|* }
10X-RAY DIFFRACTION10{ G|* }
11X-RAY DIFFRACTION11{ H|* }
12X-RAY DIFFRACTION12{ I|* }
13X-RAY DIFFRACTION13{ J|* }
14X-RAY DIFFRACTION14{ K|* }
15X-RAY DIFFRACTION15{ L|* }
16X-RAY DIFFRACTION16{ M|* }

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