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- PDB-7ta9: Crystal Structure of thymidylate synthase from Acinetobacter baumannii -

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Basic information

Entry
Database: PDB / ID: 7ta9
TitleCrystal Structure of thymidylate synthase from Acinetobacter baumannii
ComponentsThymidylate synthase
KeywordsTRANSFERASE / SSGCID / thymidylate synthase / deoxycytidylate hydroxymethylase / polypeptide binding / 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, active site / Thymidylate synthase active site. / Thymidylate synthase / Thymidylate synthase/dCMP hydroxymethylase domain / Thymidylate synthase/dCMP hydroxymethylase superfamily / Thymidylate synthase
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Thymidylate synthase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: to be published
Title: Crystal Structure of thymidylate synthase from Acinetobacter baumannii
Authors: Bolejack, M.J. / Dranow, D.M. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionDec 20, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 26, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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

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Assembly

Deposited unit
A: Thymidylate synthase
B: Thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,2777
Polymers65,7912
Non-polymers4875
Water10,539585
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5080 Å2
ΔGint3 kcal/mol
Surface area22040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.940, 73.760, 109.380
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Thymidylate synthase / TS / TSase


Mass: 32895.266 Da / Num. of mol.: 2 / Fragment: AcbaC.00249.a.B1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: thyA, thyA_1 / Plasmid: AcbaC.00249.a.B1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: V5VIF5, thymidylate synthase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 585 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.99 Å3/Da / Density % sol: 38.22 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 5
Details: Protein at 34 mg/mL was mixed 1:1 (0.4 uL protein and 0.4 uL precipitant) with 10% w/v PEG 20,000, 20% v/v PEG MME 550, 0.03 M each diethyleneglycol, triethyleneglycol, tetraethyleneglycol, ...Details: Protein at 34 mg/mL was mixed 1:1 (0.4 uL protein and 0.4 uL precipitant) with 10% w/v PEG 20,000, 20% v/v PEG MME 550, 0.03 M each diethyleneglycol, triethyleneglycol, tetraethyleneglycol, and pentaethyleneglycol, and 0.1 M MES/imidazole pH 6.5 (Morpheus E1). Cryo: Direct. Tray: 320511e1: pin: jjg2-4.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 9, 2021 / Details: Beryllium Lenses
RadiationMonochromator: Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 1.5→44.52 Å / Num. obs: 83501 / % possible obs: 98.6 % / Redundancy: 8.388 % / Biso Wilson estimate: 18.5 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.035 / Rrim(I) all: 0.038 / Χ2: 0.933 / Net I/σ(I): 38.92 / Num. measured all: 700365 / Scaling rejects: 1038
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.5-1.545.6920.563.9131285618254960.8840.60988.9
1.54-1.586.8640.445.7440727603859330.9390.47398.3
1.58-1.637.8630.3537.8145431586357780.9720.37698.6
1.63-1.688.9260.2989.7350405572456470.9840.31598.7
1.68-1.738.9240.23412.4248752552654630.990.24798.9
1.73-1.798.7850.17816.7846692536653150.9950.18899
1.79-1.868.9540.14221.4546210518651610.9960.1599.5
1.86-1.948.9370.10627.9844263498049530.9980.11299.5
1.94-2.029.0050.07435.543043480047800.9990.07999.6
2.02-2.128.5160.05942.2338986459345780.9990.06299.7
2.12-2.248.860.04651.3238929440843940.9990.04999.7
2.24-2.378.7320.03958.7735913412741130.9990.04199.7
2.37-2.548.9810.03466.48351263914391110.03699.9
2.54-2.748.5340.0371.73310203637363510.03299.9
2.74-38.6040.02780.24288653360335510.02999.9
3-3.359.0090.02591.05275593060305910.026100
3.35-3.878.4270.02296.12228722721271410.02399.7
3.87-4.748.6140.019102.7200192324232410.02100
4.74-6.718.7010.018100.44159141830182910.01999.9
6.71-44.527.8590.01699.5483541071106310.01799.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIXv4438refinement
PDB_EXTRACT3.27data extraction
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ix6

3ix6


Resolution: 1.5→44.52 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1912 2026 2.43 %
Rwork0.1624 81465 -
obs0.1631 83491 98.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 86.03 Å2 / Biso mean: 25.6334 Å2 / Biso min: 10.04 Å2
Refinement stepCycle: final / Resolution: 1.5→44.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4273 0 32 585 4890
Biso mean--41.33 33.74 -
Num. residues----535
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5-1.540.23871200.22165160528088
1.54-1.580.26651390.18565709584898
1.58-1.630.22031350.17395757589299
1.63-1.680.18461580.17255761591999
1.68-1.740.22821400.17755780592099
1.74-1.810.2161400.19195819595999
1.81-1.890.20421400.18075846598699
1.89-1.990.20441590.16875824598399
1.99-2.110.19691460.165758525998100
2.11-2.280.18311700.164858466016100
2.28-2.510.1951410.161659236064100
2.51-2.870.19451430.167459656108100
2.87-3.610.17731480.156559986146100
3.61-44.520.17551470.144862256372100
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)
11.2838-0.03280.3066.6363-3.96014.0272-0.05110.13040.1675-0.1302-0.07430.0324-0.2856-0.14770.11420.21170.0387-0.07290.1512-0.0170.194750.422358.353811.3773
21.57060.6223-0.23381.63910.69372.92270.04280.01230.1620.0354-0.15870.0702-0.1776-0.36330.11580.1490.0446-0.02050.1025-0.00970.191751.052549.446218.4211
34.5664-3.75690.97643.0902-0.81371.8389-0.02620.01470.5904-0.0296-0.0994-0.4345-0.3198-0.01620.11680.2075-0.01520.01920.14360.02940.229270.1849.15329.2559
41.66790.31550.01143.3962-0.76093.84630.0417-0.11730.18180.2687-0.0699-0.3497-0.30530.21370.04150.1406-0.0307-0.03390.14120.01470.215776.637640.096922.149
51.8824-0.79280.65532.1189-1.1721.9591-0.0037-0.0813-0.09050.049-0.0655-0.10850.08190.10360.10030.1079-0.0004-0.00130.10990.01820.120372.280127.061215.9921
61.7129-0.48431.62161.5745-1.69134.64210.00230.1581-0.064-0.095-0.0122-0.0990.16920.11560.04840.14750.01250.02110.1565-0.00130.139367.93626.82744.2802
71.81080.15311.57881.4460.34867.14230.01540.0049-0.0174-0.0383-0.0471-0.0236-0.0495-0.24750.02530.08020.0090.00590.1343-0.00380.137159.608732.575710.3023
81.2695-0.3475-0.99141.90170.8561.81770.08370.06650.1029-0.1677-0.0629-0.1015-0.1749-0.03540.04190.12380.0235-0.00480.12350.0220.130160.704144.17417.124
90.7742-0.4731-0.41731.55591.03271.8951-0.00650.01260.1266-0.0793-0.0702-0.0069-0.2263-0.05640.03180.15830.0084-0.03120.13060.0060.156255.601252.295114.9475
104.7313-4.5996-2.15435.7022.59131.84430.26440.10610.5592-0.5055-0.0468-0.4275-0.4187-0.0053-0.16160.2952-0.01130.07050.18580.0450.243870.339550.3912-0.4528
115.55073.18040.24772.8782-1.67794.68250.20040.89410.4083-0.15280.00510.5063-0.2478-0.5506-0.19550.27210.0876-0.08620.3344-0.00790.285538.861839.0355-0.1119
125.77110.4869-1.44543.1612-3.53134.0994-0.13760.178-0.2694-0.28260.18420.650.3416-0.5431-0.01840.1728-0.012-0.00990.2343-0.0640.360234.644636.266813.9618
135.19190.1819-1.34323.99471.24053.0571-0.08370.2589-0.2227-0.28230.01270.06020.0961-0.13590.05260.1484-0.0472-0.00370.137-0.02890.149643.669112.738412.3227
141.5714-0.24580.06071.991-0.02181.37620.0787-0.0143-0.07520.0168-0.09410.0270.01240.00450.00740.1019-0.0220.0030.119-0.0120.108852.119226.455718.9206
152.2640.02390.43861.6215-0.16872.90010.07050.32890.0179-0.2166-0.06520.44740.0258-0.188-0.0170.12350.014-0.04760.1807-0.05180.259537.342432.15079.9971
165.5141-0.66830.40384.1367-0.21394.3868-0.0719-0.3093-0.39840.16760.07860.94230.0663-0.5959-0.05140.2014-0.05080.08320.2434-0.05840.334632.594123.865925.4748
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -6 through 14 )A-6 - 14
2X-RAY DIFFRACTION2chain 'A' and (resid 15 through 40 )A15 - 40
3X-RAY DIFFRACTION3chain 'A' and (resid 41 through 63 )A41 - 63
4X-RAY DIFFRACTION4chain 'A' and (resid 64 through 102 )A64 - 102
5X-RAY DIFFRACTION5chain 'A' and (resid 103 through 119 )A103 - 119
6X-RAY DIFFRACTION6chain 'A' and (resid 120 through 137 )A120 - 137
7X-RAY DIFFRACTION7chain 'A' and (resid 138 through 171 )A138 - 171
8X-RAY DIFFRACTION8chain 'A' and (resid 172 through 207 )A172 - 207
9X-RAY DIFFRACTION9chain 'A' and (resid 208 through 237 )A208 - 237
10X-RAY DIFFRACTION10chain 'A' and (resid 238 through 268 )A238 - 268
11X-RAY DIFFRACTION11chain 'B' and (resid -1 through 31 )B-1 - 31
12X-RAY DIFFRACTION12chain 'B' and (resid 32 through 48 )B32 - 48
13X-RAY DIFFRACTION13chain 'B' and (resid 49 through 102 )B49 - 102
14X-RAY DIFFRACTION14chain 'B' and (resid 103 through 188 )B103 - 188
15X-RAY DIFFRACTION15chain 'B' and (resid 189 through 238 )B189 - 238
16X-RAY DIFFRACTION16chain 'B' and (resid 239 through 266 )B239 - 266

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