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- PDB-7cca: Crystal structure of White Spot Syndrome Virus Thymidylate Syntha... -

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Basic information

Entry
Database: PDB / ID: 7cca
TitleCrystal structure of White Spot Syndrome Virus Thymidylate Synthase - ternary complex with Methotrexate and dUMP
ComponentsThymidylate Synthase
KeywordsTRANSFERASE / Thymidylate Synthase / BIOSYNTHETIC PROTEIN
Function / homology
Function and homology information


thymidylate synthase / thymidylate synthase activity / dTMP biosynthetic process / dihydrofolate reductase activity / methylation / cytosol
Similarity search - Function
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
Similarity search - Domain/homology
METHOTREXATE / 2'-DEOXYURIDINE 5'-MONOPHOSPHATE / thymidylate synthase
Similarity search - Component
Biological speciesWhite spot syndrome virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsPanchal, N.V. / Kumar, S. / Shaikh, N. / Vasudevan, D.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)BT/PR23375/AAQ/3/849/2017 India
CitationJournal: Int.J.Biol.Macromol. / Year: 2021
Title: Structure analysis of thymidylate synthase from white spot syndrome virus reveals WSSV-specific structural elements.
Authors: Panchal, V. / Kumar, S. / Hossain, S.N. / Vasudevan, D.
History
DepositionJun 16, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 25, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Nov 29, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,9126
Polymers68,3872
Non-polymers1,5254
Water55831
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)92.385, 92.385, 234.720
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

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: 1 / Auth seq-ID: 1 - 286 / Label seq-ID: 1 - 286

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.640894, 0.765623, 0.055465), (0.766863, 0.63535, 0.09084), (0.03431, 0.100753, -0.99432)39.524879, -16.842871, -27.72703

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Components

#1: Protein Thymidylate Synthase / / Wsv067


Mass: 34193.332 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) White spot syndrome virus (isolate Shrimp/China/Tongan/1996)
Strain: isolate Shrimp/China/Tongan/1996 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q77J90
#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-MTX / METHOTREXATE / Methotrexate


Mass: 454.439 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H22N8O5 / Feature type: SUBJECT OF INVESTIGATION / Comment: chemotherapy*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 31 / 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: 3.66 Å3/Da / Density % sol: 66.41 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 1.1 M Ammonium tartrate dibasic

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Mar 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.75→45.36 Å / Num. obs: 24626 / % possible obs: 95.4 % / Redundancy: 4.6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.087 / Net I/σ(I): 12.7
Reflection shellResolution: 2.75→2.9 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.603 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 3858 / CC1/2: 0.711 / % possible all: 98.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACTdata extraction
iMOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7CC8

7cc8


Resolution: 2.75→45.36 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.929 / SU B: 10.61 / SU ML: 0.204 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.489 / ESU R Free: 0.286 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2278 1268 4.9 %RANDOM
Rwork0.1849 ---
obs0.1869 24626 94.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 169.72 Å2 / Biso mean: 45.284 Å2 / Biso min: 21.83 Å2
Baniso -1Baniso -2Baniso -3
1-1.09 Å20 Å2-0 Å2
2--1.09 Å2-0 Å2
3----2.17 Å2
Refinement stepCycle: final / Resolution: 2.75→45.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4636 0 106 31 4773
Biso mean--76.1 33.08 -
Num. residues----576
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0134860
X-RAY DIFFRACTIONr_bond_other_d0.0040.0174486
X-RAY DIFFRACTIONr_angle_refined_deg1.7421.6656573
X-RAY DIFFRACTIONr_angle_other_deg1.2961.58810393
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.185574
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.31621.538260
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.83115845
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3761536
X-RAY DIFFRACTIONr_chiral_restr0.0690.2602
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025382
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021076
Refine LS restraints NCSNumber: 2304 / Type: TIGHT THERMAL / Rms dev position: 6.68 Å / Weight position: 0.5
LS refinement shellResolution: 2.75→2.821 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 93 -
Rwork0.287 1858 -
all-1951 -
obs--98.39 %

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