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- PDB-3v8h: Crystal structure of Thymidylate Synthase from Burkholderia thail... -

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Basic information

Entry
Database: PDB / ID: 3v8h
TitleCrystal structure of Thymidylate Synthase from Burkholderia thailandensis
ComponentsThymidylate synthase
KeywordsTRANSFERASE / SSGCID / Thymidylate synthase / 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 / Thymidylate synthase/dCMP hydroxymethylase domain / Thymidylate synthase/dCMP hydroxymethylase superfamily / Thymidylate synthase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
CITRIC ACID / Thymidylate synthase
Similarity search - Component
Biological speciesBurkholderia thailandensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.65 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Plos One / Year: 2013
Title: Combining functional and structural genomics to sample the essential Burkholderia structome.
Authors: Baugh, L. / Gallagher, L.A. / Patrapuvich, R. / Clifton, M.C. / Gardberg, A.S. / Edwards, T.E. / Armour, B. / Begley, D.W. / Dieterich, S.H. / Dranow, D.M. / Abendroth, J. / Fairman, J.W. / ...Authors: Baugh, L. / Gallagher, L.A. / Patrapuvich, R. / Clifton, M.C. / Gardberg, A.S. / Edwards, T.E. / Armour, B. / Begley, D.W. / Dieterich, S.H. / Dranow, D.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Staker, B.L. / Phan, I. / Gillespie, A. / Choi, R. / Nakazawa-Hewitt, S. / Nguyen, M.T. / Napuli, A. / Barrett, L. / Buchko, G.W. / Stacy, R. / Myler, P.J. / Stewart, L.J. / Manoil, C. / Van Voorhis, W.C.
History
DepositionDec 22, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2013Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_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
C: Thymidylate synthase
D: Thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,81713
Polymers147,8684
Non-polymers9499
Water20,9331162
1
A: Thymidylate synthase
D: Thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,3747
Polymers73,9342
Non-polymers4405
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6840 Å2
ΔGint-17 kcal/mol
Surface area23850 Å2
MethodPISA
2
B: Thymidylate synthase
C: Thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,4426
Polymers73,9342
Non-polymers5084
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6910 Å2
ΔGint-24 kcal/mol
Surface area23400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.060, 107.690, 117.240
Angle α, β, γ (deg.)90.000, 98.060, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Thymidylate synthase / / TS / TSase


Mass: 36967.008 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia thailandensis (bacteria) / Strain: E264/ATCC 700388/DSM 13276/CIP 106301 / Gene: thyA, BTH_I1680 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q2SXY2, thymidylate synthase
#2: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1162 / Source method: isolated from a natural source / Formula: H2O

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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: 2.5 Å3/Da / Density % sol: 50.73 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: Internal tracking number 225920_a2. JCSG well A2. 0.1M Ammonium Citric / Citric Acid pH 5.5, 20% w/v PEG 3,000, 25% Ethylene Glycol as Cryo. Protein ButhA.01181.a.A1 PS01191 51.93mg/ml., ...Details: Internal tracking number 225920_a2. JCSG well A2. 0.1M Ammonium Citric / Citric Acid pH 5.5, 20% w/v PEG 3,000, 25% Ethylene Glycol as Cryo. Protein ButhA.01181.a.A1 PS01191 51.93mg/ml., vapor diffusion, sitting drop, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 11, 2011
RadiationMonochromator: Si(220) Asymmetric cut single crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 1.65→49.51 Å / Num. all: 174129 / Num. obs: 166030 / % possible obs: 95.3 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4.82 % / Biso Wilson estimate: 25.782 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 14.95
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.65-1.690.532.5511451173591.4
1.69-1.740.4413.1521131158892.5
1.74-1.790.3643.8527461137293.2
1.79-1.840.2884.9528291107893.9
1.84-1.910.2316.1528331083694.4
1.91-1.970.1728.3518601051795
1.97-2.050.14110.2508861022395.3
2.05-2.130.11712.449035983895.7
2.13-2.220.09814.747399947096.2
2.22-2.330.08516.745584914896.4
2.33-2.460.07618.343534873696.8
2.46-2.610.06520.940820825197.2
2.61-2.790.05823.138456779797.3
2.79-3.010.0526.135590726397.4
3.01-3.30.04329.232560671797.8
3.3-3.690.03932.128363604497.1
3.69-4.260.03434.725727538298.1
4.26-5.220.0336.822743457898.4
5.22-7.380.0335.617983357798.6
7.380.02637.99214188092.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å19.84 Å
Translation2.5 Å19.84 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
REFMAC5.6.0117refinement
PDB_EXTRACT3.004data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1tis

1tis


Resolution: 1.65→49.51 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.949 / SU B: 3.346 / SU ML: 0.058 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / ESU R: 0.092 / ESU R Free: 0.091 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.203 8295 5 %RANDOM
Rwork0.175 ---
all0.178 174129 --
obs0.177 166030 95.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.469 Å2
Baniso -1Baniso -2Baniso -3
1-1.53 Å20 Å20.4 Å2
2---0.15 Å20 Å2
3----1.26 Å2
Refinement stepCycle: LAST / Resolution: 1.65→49.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9470 0 63 1162 10695
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0199894
X-RAY DIFFRACTIONr_bond_other_d0.0010.026772
X-RAY DIFFRACTIONr_angle_refined_deg1.5061.95413473
X-RAY DIFFRACTIONr_angle_other_deg0.923316300
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.00751232
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.00322.656482
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.869151538
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3381599
X-RAY DIFFRACTIONr_chiral_restr0.0910.21456
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02111190
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022245
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 598 -
Rwork0.28 10928 -
all-11526 -
obs--91.14 %
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)
10.77761.0380.52212.26920.47251.9867-0.12220.08780.0354-0.23330.15440.2787-0.5508-0.2306-0.03220.18930.0467-0.04160.09730.03410.093824.560456.015598.4643
20.143-0.0035-0.10450.4636-0.42841.2231-0.01610.0399-0.044-0.0031-0.0213-0.02690.02640.07110.03740.0327-0.00040.00150.0431-0.00650.042644.077433.2223106.8275
30.4410.18070.01170.44490.02280.855-0.04760.0351-0.0617-0.08570.0460.0961-0.0252-0.11490.00160.0209-0.0188-0.01380.0647-0.0020.092125.181440.0211103.2298
42.13392.0777-1.02193.61-0.37891.7249-0.28340.0511-0.0751-0.31640.1529-0.43810.63660.39690.13050.30730.16660.1420.21110.02950.169914.078927.355746.5629
50.1002-0.0937-0.10530.45920.17641.18770.01890.04080.0381-0.0207-0.0135-0.0395-0.02840.0006-0.00540.0195-0.010.00490.05020.0020.043-4.996949.299950.9517
60.36490.3488-0.46780.8297-0.35351.6218-0.060.00030.0349-0.11060.0098-0.19960.2070.26110.05010.04160.01540.03030.14410.01450.17314.436743.116348.9336
71.23991.369-0.01053.11070.93431.22570.1341-0.2285-0.19340.2903-0.0665-0.47930.2320.388-0.06770.07760.0531-0.05380.1840.03790.132313.997330.003469.9301
80.0786-0.01090.04970.22470.06911.0088-0.02920.0109-0.00980.06690.00510.0680.0385-0.01150.02410.0486-0.01360.00680.0367-0.00130.0415-12.748239.520163.799
90.9690.1904-0.61111.07580.08780.7323-0.0295-0.0745-0.02380.1374-0.0053-0.00590.14930.09630.03480.0850.00780.00730.0224-0.00590.0264-3.340322.486765.514
102.91993.82260.21195.72040.19650.5260.1837-0.12020.32650.2526-0.19540.5929-0.1626-0.28940.01170.07750.08640.03820.176-0.02430.175417.698255.0649119.8689
110.13120.0424-0.17960.2675-0.02260.7125-0.02290.005-0.00910.09720.0081-0.0618-0.04590.02580.01480.0727-0.0056-0.00640.03940.00010.056545.161644.0246122.9633
120.48380.20650.41030.90670.08040.7837-0.0101-0.04650.02610.1309-0.01260.0601-0.157-0.09970.02270.080.00610.0080.02760.00230.045734.841360.7894122.3287
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 50
2X-RAY DIFFRACTION2A51 - 157
3X-RAY DIFFRACTION3A158 - 314
4X-RAY DIFFRACTION4B1 - 50
5X-RAY DIFFRACTION5B51 - 188
6X-RAY DIFFRACTION6B189 - 314
7X-RAY DIFFRACTION7C2 - 51
8X-RAY DIFFRACTION8C52 - 192
9X-RAY DIFFRACTION9C193 - 310
10X-RAY DIFFRACTION10D2 - 42
11X-RAY DIFFRACTION11D43 - 193
12X-RAY DIFFRACTION12D194 - 310

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