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- PDB-2ftq: E. coli thymidylate synthase at 1.8 A resolution -

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Basic information

Entry
Database: PDB / ID: 2ftq
TitleE. coli thymidylate synthase at 1.8 A resolution
ComponentsThymidylate synthase
KeywordsTRANSFERASE / methyltransferase
Function / homology
Function and homology information


thymidylate synthase / thymidylate synthase activity / dTMP biosynthetic process / dTTP biosynthetic process / response to radiation / regulation of translation / methylation / magnesium ion binding / protein homodimerization activity / RNA binding / cytosol
Similarity search - Function
Thymidylate Synthase; Chain A / Thymidylate synthase/dCMP hydroxymethylase domain / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Thymidylate synthase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / isomorphous / Resolution: 1.81 Å
AuthorsMontfort, W.R. / Roberts, S.A.
CitationJournal: To be Published
Title: Subtle Conformational Differences between Escherichia coli Thymidylate Synthase and Specific Mutants of this Enzyme
Authors: Montfort, W.R. / Roberts, S.A.
History
DepositionJan 24, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 2, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2318
Polymers30,5601
Non-polymers6717
Water3,603200
1
A: Thymidylate synthase
hetero molecules

A: Thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,46216
Polymers61,1192
Non-polymers1,34314
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation14_555-x,-y+1/2,z1
Buried area6760 Å2
ΔGint-162 kcal/mol
Surface area21430 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)131.234, 131.234, 131.234
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number199
Space group name H-MI213
DetailsThe biological assembly is a dimer. There is one monomer in the asymetric unit. To generate the second monomer of the dimer, apply the symmetry operation -x,1/2-y,z

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Components

#1: Protein Thymidylate synthase / / TS / TSase


Mass: 30559.666 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: thyA / Plasmid: BLUSCRIPT SK+ / Production host: Escherichia coli (E. coli) / Strain (production host): Xac25 Thy / References: UniProt: P0A884, thymidylate synthase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 200 / 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: 3.08 Å3/Da / Density % sol: 60.07 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 2.5 M ammonium sulfate, 20 mM KH2PO4, 4 mM DTT, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 24, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.81→21.87 Å / Num. all: 34259 / Num. obs: 34259 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 16
Reflection shellResolution: 1.81→1.87 Å / Redundancy: 9 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 2.4 / Num. unique all: 3420 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
d*TREKdata scaling
RefinementMethod to determine structure: isomorphous / Resolution: 1.81→21.9 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.949 / SU B: 5.073 / SU ML: 0.084 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.123 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS, TLS REFINEMENT
RfactorNum. reflection% reflectionSelection details
Rfree0.22556 1728 5 %RANDOM
Rwork0.20194 ---
obs0.20316 32531 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.978 Å2
Refinement stepCycle: LAST / Resolution: 1.81→21.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2153 0 35 200 2388
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0222357
X-RAY DIFFRACTIONr_bond_other_d0.0020.021604
X-RAY DIFFRACTIONr_angle_refined_deg1.6531.9553220
X-RAY DIFFRACTIONr_angle_other_deg1.06333902
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8355291
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.77723.636121
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.07815399
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4911518
X-RAY DIFFRACTIONr_chiral_restr0.1070.2335
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022616
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02499
X-RAY DIFFRACTIONr_nbd_refined0.2230.2451
X-RAY DIFFRACTIONr_nbd_other0.2080.21623
X-RAY DIFFRACTIONr_nbtor_refined0.170.21060
X-RAY DIFFRACTIONr_nbtor_other0.0850.21173
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1380.2166
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.20.223
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2530.2114
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.140.220
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0141.51811
X-RAY DIFFRACTIONr_mcbond_other0.2951.5551
X-RAY DIFFRACTIONr_mcangle_it1.24822239
X-RAY DIFFRACTIONr_scbond_it2.26831146
X-RAY DIFFRACTIONr_scangle_it3.0684.5968
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.81→1.857 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.445 138 -
Rwork0.384 2421 -
obs--100 %
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)
11.26980.34710.05711.0704-0.37530.9317-0.01630.1318-0.1648-0.1517-0.0204-0.14190.0750.1860.0367-0.1114-0.02160.0135-0.0559-0.0189-0.123614.94129.77153.931
23.8517-0.0021.12359.00178.240611.21960.1450.13440.3081-0.1804-0.06980.0789-0.1915-0.0791-0.0752-0.0807-0.06450.0209-0.06560.0602-0.08737.00250.46552.571
32.57191.3897-1.11321.8684-0.82891.25890.1134-0.1938-0.00870.1912-0.0805-0.1181-0.11740.1708-0.0329-0.1243-0.0279-0.0275-0.07490.0228-0.102916.70331.89672.524
41.991.29240.8862.61611.28242.53220.012-0.13590.05160.0487-0.0652-0.0031-0.0704-0.08880.0531-0.1403-0.012-0.0043-0.10720.0105-0.15233.91731.96769.176
517.8342-7.3306-13.636122.463223.958827.74550.52350.24850.5121-0.1235-0.61490.3319-0.4621-0.78110.0914-0.0365-0.04660.0196-0.05560.0178-0.102420.25552.35360.188
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 91 - 9
2X-RAY DIFFRACTION1AA25 - 5025 - 50
3X-RAY DIFFRACTION1AA118 - 122118 - 122
4X-RAY DIFFRACTION1AA150 - 260150 - 260
5X-RAY DIFFRACTION2AA10 - 2410 - 24
6X-RAY DIFFRACTION3AA51 - 11751 - 117
7X-RAY DIFFRACTION4AA123 - 149123 - 149
8X-RAY DIFFRACTION5AA261 - 264261 - 264

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