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- PDB-6k7s: Crystal structure of thymidylate synthase from shrimp -

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Basic information

Entry
Database: PDB / ID: 6k7s
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
TOMUDEX / 2'-DEOXYURIDINE 5'-MONOPHOSPHATE / Thymidylate synthase / Thymidylate synthase
Similarity search - Component
Biological speciesPenaeus vannamei (Pacific white shrimp)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.56 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,9806
Polymers67,4472
Non-polymers1,5334
Water8,665481
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7270 Å2
ΔGint-33 kcal/mol
Surface area21620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.653, 83.674, 55.157
Angle α, β, γ (deg.)90.00, 92.26, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Thymidylate synthase /


Mass: 33723.430 Da / Num. of mol.: 2
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-UMP / 2'-DEOXYURIDINE 5'-MONOPHOSPHATE / DUMP / Deoxyuridine monophosphate


Mass: 308.182 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H13N2O8P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-D16 / TOMUDEX / ZD1694 / Raltitrexed / Raltitrexed


Mass: 458.488 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H22N4O6S / Feature type: SUBJECT OF INVESTIGATION / Comment: chemotherapy, inhibitor*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 481 / 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: 2.12 Å3/Da / Density % sol: 41.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: The drop contained 1 ul protein solution (10 mg/ml protein + 5 mM dUMP + 5 mM raltitrexed incubated for 4 h at 4 degrees) and 1 ul reservoir solution (20% (w/v) PEG 3350, 200 mM ammonium citrate, pH 7.0)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 1.56→43.437 Å / Num. obs: 72920 / % possible obs: 94.4 % / Redundancy: 7.1 % / CC1/2: 0.998 / Rpim(I) all: 0.022 / Rrim(I) all: 0.06 / Rsym value: 0.056 / Net I/σ(I): 18.5
Reflection shellResolution: 1.56→1.587 Å / Redundancy: 6.5 % / Mean I/σ(I) obs: 3.8 / Num. unique obs: 3126 / CC1/2: 0.94 / Rpim(I) all: 0.155 / Rrim(I) all: 0.403 / Rsym value: 0.371 / % possible all: 80.6

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSJan 26, 2018 (BUILT 20180409)data reduction
Aimless(version 0.5.29), CCP4 7.0.024data scaling
PHASER2.7.17phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6K7R

6k7r


Resolution: 1.56→42.487 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 19.13
RfactorNum. reflection% reflectionSelection details
Rfree0.1984 3552 4.87 %random
Rwork0.1602 ---
obs0.1621 72911 94.39 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.56→42.487 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4576 0 104 484 5164
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094834
X-RAY DIFFRACTIONf_angle_d1.2356545
X-RAY DIFFRACTIONf_dihedral_angle_d16.7872884
X-RAY DIFFRACTIONf_chiral_restr0.058666
X-RAY DIFFRACTIONf_plane_restr0.008867
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5597-1.58110.22041080.18682341X-RAY DIFFRACTION78
1.5811-1.60370.22051450.17332653X-RAY DIFFRACTION93
1.6037-1.62760.19981460.16842805X-RAY DIFFRACTION95
1.6276-1.6530.22141230.17862783X-RAY DIFFRACTION95
1.653-1.68010.24031390.17342801X-RAY DIFFRACTION95
1.6801-1.70910.2371250.17462820X-RAY DIFFRACTION95
1.7091-1.74020.21591270.17152813X-RAY DIFFRACTION96
1.7402-1.77370.20031460.162796X-RAY DIFFRACTION95
1.7737-1.80990.20451060.1682740X-RAY DIFFRACTION93
1.8099-1.84920.17241560.16932760X-RAY DIFFRACTION95
1.8492-1.89220.1981740.18342814X-RAY DIFFRACTION96
1.8922-1.93960.21321250.16532814X-RAY DIFFRACTION96
1.9396-1.9920.19411260.1612858X-RAY DIFFRACTION96
1.992-2.05060.19681610.16532815X-RAY DIFFRACTION96
2.0506-2.11680.21031370.16432790X-RAY DIFFRACTION95
2.1168-2.19250.1871390.15452687X-RAY DIFFRACTION91
2.1925-2.28020.16921560.15672855X-RAY DIFFRACTION97
2.2802-2.3840.19271670.1552832X-RAY DIFFRACTION97
2.384-2.50970.19441630.15442833X-RAY DIFFRACTION96
2.5097-2.66690.20151450.1592785X-RAY DIFFRACTION96
2.6669-2.87280.18431500.16352678X-RAY DIFFRACTION92
2.8728-3.16180.20971480.16772876X-RAY DIFFRACTION97
3.1618-3.61910.20191490.15842832X-RAY DIFFRACTION96
3.6191-4.55880.18571400.13862725X-RAY DIFFRACTION92
4.5588-42.50250.20991510.16462853X-RAY DIFFRACTION95
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)
10.5829-0.09110.26760.20670.1570.28840.0384-0.10840.05480.0029-0.07970.0915-0.0554-0.0556-0.00030.1291-0.00390.01250.1525-0.01710.142915.34289.144620.3084
20.3940.30860.03180.4247-0.23150.3668-0.14330.31390.2591-0.24560.07180.0460.1518-0.0364-0.12130.2138-0.0117-0.04680.29070.04180.139215.43590.6427-4.4052
30.87420.06560.22690.3745-0.00590.31060.04840.0841-0.0205-0.1099-0.03980.03440.0616-0.02990.00120.12120.008-0.00290.08360.00230.082820.9646-1.362910.4453
40.31310.2748-0.05040.3062-0.21280.22830.1004-0.059-0.1306-0.1803-0.08720.20720.0247-0.20530.00850.1699-0.0142-0.04420.2177-0.0320.24624.2876-6.101512.0144
50.0038-0.00340.00270.00360.0020.0059-0.04520.0914-0.03680.01740.0289-0.0246-0.0130.115700.38730.0101-0.10160.39620.05260.27118.512517.72287.1895
60.1880.082800.0471-0.02290.09370.1429-0.1747-0.03940.135-0.17730.04090.0534-0.0724-0.00020.2015-0.02360.00460.17620.00760.154533.0333-4.740331.6114
70.02090.02630.00320.00580.00980.0040.0612-0.19770.07560.0411-0.09780.0130.0237-0.037-00.1245-0.00710.01140.122-0.02050.136434.95758.701425.7102
80.19760.3010.00830.39490.05080.13220.01570.0869-0.1039-0.003-0.0126-0.11630.08670.1315-0.08070.13260.05860.01690.2541-0.01920.178950.852-2.56949.8051
90.79320.17460.16680.20150.0480.13150.01780.06990.0407-0.0408-0.0387-0.09730.01150.0772-0.00010.13740.01210.01980.11450.01140.130937.51466.36214.2912
100.6742-0.09620.3350.41830.12360.19160.11240.00080.06060.165-0.1072-0.1753-0.00620.07150.05850.1677-0.0181-0.02390.18790.0080.173248.60917.159927.651
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 1:52)
2X-RAY DIFFRACTION2(chain A and resid 53:130)
3X-RAY DIFFRACTION3(chain A and resid 131:245)
4X-RAY DIFFRACTION4(chain A and resid 246:282)
5X-RAY DIFFRACTION5(chain A and resid 283:289)
6X-RAY DIFFRACTION6(chain B and resid 1:32)
7X-RAY DIFFRACTION7(chain B and resid 33:48)
8X-RAY DIFFRACTION8(chain B and resid 49:132)
9X-RAY DIFFRACTION9(chain B and resid 133:238)
10X-RAY DIFFRACTION10(chain B and resid 239:288)

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