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- PDB-7xyj: Structure of WSSV thymidylate synthase in complex with dUMP -

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Basic information

Entry
Database: PDB / ID: 7xyj
TitleStructure of WSSV thymidylate synthase in complex with dUMP
ComponentsThymidylate synthase
KeywordsTRANSFERASE / white spot syndrome virus / dTTP / nucleotide biosynthesis
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
2'-DEOXYURIDINE 5'-MONOPHOSPHATE / thymidylate synthase
Similarity search - Component
Biological speciesWhite spot syndrome virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.275 Å
AuthorsMa, Q. / Liu, C. / Zang, K.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Structure of WSSV thymidylate synthase in complex with dUMP
Authors: Ma, Q. / Liu, C. / Zang, K.
History
DepositionJun 1, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 7, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,66219
Polymers133,5784
Non-polymers3,08515
Water3,495194
1
A: Thymidylate synthase
B: Thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,9787
Polymers66,7892
Non-polymers1,1895
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6760 Å2
ΔGint-37 kcal/mol
Surface area22040 Å2
MethodPISA
2
C: Thymidylate synthase
D: Thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,68512
Polymers66,7892
Non-polymers1,89610
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7860 Å2
ΔGint-57 kcal/mol
Surface area22390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.910, 132.350, 234.110
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Thymidylate synthase /


Mass: 33394.453 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) White spot syndrome virus / Strain: isolate Shrimp/China/Tongan/1996 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q77J90, thymidylate synthase

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Non-polymers , 5 types, 209 molecules

#2: Chemical
ChemComp-UMP / 2'-DEOXYURIDINE 5'-MONOPHOSPHATE / DUMP / Deoxyuridine monophosphate


Mass: 308.182 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H13N2O8P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER / Bis-tris methane


Mass: 209.240 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 194 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.18 Å3/Da / Density % sol: 61.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: The protein in complex with dUMP was crystallized in drops containing 1 ul protein solution (10 mg/ml protein + 5 mM dUMP incubated at 4 degrees for 4 h) and 1 ul reservoir solution (100 mM ...Details: The protein in complex with dUMP was crystallized in drops containing 1 ul protein solution (10 mg/ml protein + 5 mM dUMP incubated at 4 degrees for 4 h) and 1 ul reservoir solution (100 mM Bis-Tris pH 6.5, 25% (w/v) PEG 3350, 200 mM Li2SO4).

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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 PILATUS 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: 2.275→117.054 Å / Num. obs: 79528 / % possible obs: 100 % / Redundancy: 13.2 % / CC1/2: 0.999 / Rpim(I) all: 0.02 / Rrim(I) all: 0.073 / Rsym value: 0.07 / Net I/σ(I): 22.2
Reflection shellResolution: 2.275→2.282 Å / Redundancy: 12.4 % / Mean I/σ(I) obs: 2 / Num. unique obs: 775 / CC1/2: 0.902 / Rpim(I) all: 0.341 / Rrim(I) all: 1.21 / Rsym value: 1.159 / % possible all: 99

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
PDB_EXTRACT3.27data extraction
XDSJan 26, 2018, built on 20180409data reduction
Aimlessversion 0.5.29data scaling
PHASER2.7.17phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6K7R

6k7r


Resolution: 2.275→117.054 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.937 / SU R Cruickshank DPI: 0.203 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.201 / SU Rfree Blow DPI: 0.16 / SU Rfree Cruickshank DPI: 0.163
RfactorNum. reflection% reflectionSelection details
Rfree0.208 3955 4.98 %RANDOM
Rwork0.188 ---
obs0.189 79438 99.3 %-
Displacement parametersBiso max: 157.13 Å2 / Biso mean: 60.93 Å2 / Biso min: 33.9 Å2
Baniso -1Baniso -2Baniso -3
1--10.7716 Å20 Å20 Å2
2---5.2111 Å20 Å2
3---15.9827 Å2
Refine analyzeLuzzati coordinate error obs: 0.29 Å
Refinement stepCycle: final / Resolution: 2.275→117.054 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9026 0 213 194 9433
Biso mean--76.77 54.96 -
Num. residues----1120
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d3367SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes216HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1376HARMONIC5
X-RAY DIFFRACTIONt_it9455HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1168SEMIHARMONIC5
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_contact10540SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d9455HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg12762HARMONIC21.08
X-RAY DIFFRACTIONt_omega_torsion3.45
X-RAY DIFFRACTIONt_other_torsion17.89
LS refinement shellResolution: 2.275→2.33 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.279 286 5.38 %
Rwork0.214 5031 -
obs--91.7 %
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)
11.2584-0.0347-0.60881.9565-0.25592.00470.1337-0.20230.10560.6157-0.1157-0.0505-0.3150.2231-0.018-0.0298-0.0744-0.0061-0.2337-0.0647-0.292513.519846.053545.8567
21.10210.3986-0.53471.52760.01741.77630.08430.04620.142-0.209-0.0280.0942-0.2539-0.0887-0.0563-0.13480.0560.0068-0.22460.0281-0.213412.36646.89217.7702
31.00960.22120.34441.4974-0.26391.8316-0.0728-0.2385-0.07090.25190.04890.03480.1048-0.09630.0239-0.13720.0210.0476-0.1740.0588-0.26285.73480.079840.3581
41.119-0.15430.07831.2385-0.33561.9219-0.03190.2099-0.1612-0.13420.00570.06530.31260.04920.0262-0.1719-0.01140.0069-0.18950.0013-0.20155.821-1.252112.2594
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A-2 - 280
2X-RAY DIFFRACTION2{ B|* }B2 - 280
3X-RAY DIFFRACTION3{ C|* }C1 - 280
4X-RAY DIFFRACTION4{ D|* }D3 - 280

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