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- PDB-3ix6: Crystal structure of Thymidylate synthase thyA from Brucella meli... -

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Basic information

Entry
Database: PDB / ID: 3ix6
TitleCrystal structure of Thymidylate synthase thyA from Brucella melitensis
ComponentsThymidylate synthase
KeywordsTRANSFERASE / NIAID / SSGCID / Seattle Structural Center for Infectious Disease / brucellosis / orchitis / epididymitis / mastitis / thymidylate / Methyltransferase / Nucleotide biosynthesis / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


thymidylate synthase / thymidylate synthase activity / dTMP biosynthetic process / dTTP biosynthetic process / methylation / cytoplasm
Similarity search - Function
Thymidylate Synthase; Chain A / Thymidylate synthase/dCMP hydroxymethylase domain / 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
Similarity search - Component
Biological speciesBrucella melitensis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Crystal structure of Thymidylate synthase thyA from Brucella melitensis
Authors: Abendroth, J. / Edwards, T.E. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
History
DepositionSep 3, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 22, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_special_symmetry
Item: _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


Theoretical massNumber of molelcules
Total (without water)82,9422
Polymers82,9422
Non-polymers00
Water4,143230
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4320 Å2
ΔGint-15 kcal/mol
Surface area20090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.600, 62.190, 85.960
Angle α, β, γ (deg.)90.000, 108.880, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-342-

HOH

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Components

#1: Protein Thymidylate synthase / / TS / TSase


Mass: 41471.207 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella melitensis (bacteria) / Gene: thyA, BMEI0608 / Plasmid: pBADSmt / Production host: Escherichia coli (E. coli) / References: UniProt: P67042, thymidylate synthase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 230 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAUTHORS STATE THAT THE TARGET PROTEIN (TARGETDB BRMEA.00249.A) WAS EXPRESSED WITH AN N-TERMINAL HIS ...AUTHORS STATE THAT THE TARGET PROTEIN (TARGETDB BRMEA.00249.A) WAS EXPRESSED WITH AN N-TERMINAL HIS TAG AND SMT3 FUSION PROTEIN, WHICH IS TYPICALLY REMOVED BY ULP-1 PROTEASE. FOR A SIGNIFICANT PORTION OF THE SAMPLE THE TAG AND FUSION PROTEIN WERE NOT CLEAVED DURING THE PURIFICATION. IT APPEARS THAT THE FUSION PROTEIN (I.E. THE FIRST ~93 AMINO ACIDS) IS IN THE CRYSTAL LATTICE, BUT THAT THE SMT3 FUSION PROTEIN IS LARGELY DISORDERED.

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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: 2.36 Å3/Da / Density % sol: 47.82 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: JCSG+ condition G6, 0.2 M sodium malonate pH 7.0, 20% PEG 3350, Crystal tracking ID 204287g6, 24.5 mg/mL protein concentration, crystallized with the His6-Smt3 fusion tag still on, VAPOR ...Details: JCSG+ condition G6, 0.2 M sodium malonate pH 7.0, 20% PEG 3350, Crystal tracking ID 204287g6, 24.5 mg/mL protein concentration, crystallized with the His6-Smt3 fusion tag still on, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Aug 17, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 2.2 Å / Num. obs: 39043 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.051 / Net I/σ(I): 19.93
Reflection shellResolution: 2.2→2.26 Å / Rmerge(I) obs: 0.362 / Mean I/σ(I) obs: 3.48 / Num. unique all: 2657 / % possible all: 91.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.914 / Highest resolution: 2.2 Å / WRfactor Rfree: 0.219 / WRfactor Rwork: 0.196 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.848 / SU B: 9.886 / SU ML: 0.115 / SU R Cruickshank DPI: 0.214 / SU Rfree: 0.183 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.214 / ESU R Free: 0.183 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.245 1950 5 %RANDOM
Rwork0.213 ---
obs0.215 39042 99.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 55.15 Å2 / Biso mean: 19.567 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å20.03 Å2
2---0.09 Å20 Å2
3---0.05 Å2
Refinement stepCycle: LAST / Highest resolution: 2.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3894 0 0 230 4124
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0214005
X-RAY DIFFRACTIONr_angle_refined_deg1.2561.9385460
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7555486
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.33223.52196
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.73515594
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7981524
X-RAY DIFFRACTIONr_chiral_restr0.0850.2594
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213126
X-RAY DIFFRACTIONr_mcbond_it0.6761.52446
X-RAY DIFFRACTIONr_mcangle_it1.26423911
X-RAY DIFFRACTIONr_scbond_it1.7931559
X-RAY DIFFRACTIONr_scangle_it2.8134.51549
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.323 128 -
Rwork0.27 2499 -
all-2627 -
obs--91.25 %
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)
10.8933-0.155-0.0591.6999-0.35380.8609-0.0146-0.11770.09090.11440.05170.0116-0.1119-0.0835-0.03710.05270.0392-0.01410.0973-0.03190.054634.438432.830636.6743
21.92971.48980.79191.89370.71313.9327-0.24050.1541-0.0526-0.07530.10380.19020.2397-0.49630.13670.0886-0.08010.02430.1515-0.03710.15132.12279.129128.2494
30.3334-0.0058-0.17631.36660.20120.5695-0.08460.0646-0.0867-0.11180.0962-0.08840.0323-0.0686-0.01160.0457-0.01670.0010.0954-0.04440.087842.15320.381326.7698
43.4007-1.4486-0.84143.8586-0.01351.5795-0.2061-0.2976-0.34890.52690.2867-0.05740.2008-0.0866-0.08050.10220.0183-0.03540.05250.03720.079540.987710.51241.3587
521.9158-11.38554.853218.3108-2.62881.1383-0.8003-0.92482.05480.60660.5308-0.8719-0.3477-0.24940.26950.72710.14560.12510.1837-0.07670.490748.531848.962533.9026
63.406-2.32661.1632.2876-0.58151.6081-0.1736-0.28860.18070.02540.2928-0.2337-0.18850.0352-0.11920.0741-0.0033-0.02270.0676-0.07060.110751.769139.770132.8117
71.48830.36140.39633.96610.5361.27690.07130.3695-0.0178-0.6595-0.0366-0.817-0.09690.0834-0.03470.208-0.0170.14580.13370.01740.174552.205436.55377.4526
80.3476-0.37920.32591.2176-0.19241.2543-0.03680.06070.0329-0.26150.0689-0.2061-0.2711-0.003-0.03210.1795-0.03190.03380.0717-0.02480.074345.768741.130818.9641
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 41
2X-RAY DIFFRACTION2A42 - 87
3X-RAY DIFFRACTION3A88 - 218
4X-RAY DIFFRACTION4A219 - 251
5X-RAY DIFFRACTION5B-5 - 4
6X-RAY DIFFRACTION6B5 - 42
7X-RAY DIFFRACTION7B43 - 113
8X-RAY DIFFRACTION8B114 - 251

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