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- PDB-3bhr: E. coli TS complexed with 5-NO2dUMP and tetrahydrofolate at 1.9 A... -

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Basic information

Entry
Database: PDB / ID: 3bhr
TitleE. coli TS complexed with 5-NO2dUMP and tetrahydrofolate at 1.9 A resolution (space group 152)
ComponentsThymidylate synthase
KeywordsTRANSFERASE / methyltransferase / Nucleotide biosynthesis / Repressor / RNA-binding / Translation regulation
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
2'-DEOXY-5-NITROURIDINE 5'-MONOPHOSPHATE / PHOSPHATE ION / (6S)-5,6,7,8-TETRAHYDROFOLATE / Thymidylate synthase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.9 Å
AuthorsRoberts, S.A. / Montfort, W.R.
CitationJournal: To be Published
Title: Structural Studies of Early Events in Catalysis by Thymidylate Synthase
Authors: Arendall III, W.B. / Hyatt, D.C. / Roberts, S.A. / Weichsel, A. / Dahlgren, A.L. / Maley, F. / Montfort, W.R.
History
DepositionNov 28, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 2, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Apr 18, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector

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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)31,5505
Polymers30,5601
Non-polymers9914
Water1,802100
1
A: Thymidylate synthase
hetero molecules

A: Thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,10010
Polymers61,1192
Non-polymers1,9818
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+2/31
Buried area8660 Å2
ΔGint-36 kcal/mol
Surface area19240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.950, 71.950, 115.470
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-297-

HOH

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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.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-THG / (6S)-5,6,7,8-TETRAHYDROFOLATE


Mass: 445.429 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H23N7O6
#4: Chemical ChemComp-NDU / 2'-DEOXY-5-NITROURIDINE 5'-MONOPHOSPHATE


Type: DNA linking / Mass: 355.195 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N3O10P
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 100 / 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: 2.82 Å3/Da / Density % sol: 56.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 2.5 M ammonium sulfate, 20 mM KH2PO4, 4MM DTT, 4MM 5-NO2dUMP, 4MM MTF, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.5418 Å
DetectorType: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER / Date: Nov 1, 1996
RadiationMonochromator: graphite crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→62.02 Å / Num. all: 25412 / Num. obs: 25412 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Rmerge(I) obs: 0.66 / Net I/σ(I): 11.1

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Processing

Software
NameVersionClassification
REFMAC5.3.0037refinement
MADNESSdata collection
PROCORdata reduction
PROCORdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.9→10 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.952 / SU B: 2.864 / SU ML: 0.081 / Cross valid method: THROUGHOUT / ESU R: 0.134 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20132 1278 5.1 %RANDOM
Rwork0.16663 ---
obs0.1684 23761 89.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.933 Å2
Baniso -1Baniso -2Baniso -3
1-0.56 Å20.28 Å20 Å2
2--0.56 Å20 Å2
3----0.84 Å2
Refinement stepCycle: LAST / Resolution: 1.9→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2153 0 65 100 2318
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0212294
X-RAY DIFFRACTIONr_bond_other_d0.0020.021535
X-RAY DIFFRACTIONr_angle_refined_deg1.8121.9793120
X-RAY DIFFRACTIONr_angle_other_deg1.58233723
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3015262
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.68424.66103
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.55515354
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.3461513
X-RAY DIFFRACTIONr_chiral_restr0.2480.2322
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212530
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02480
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.275
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1410.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2940.272
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1530.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9351.51323
X-RAY DIFFRACTIONr_mcbond_other0.2491.5534
X-RAY DIFFRACTIONr_mcangle_it1.77622140
X-RAY DIFFRACTIONr_scbond_it2.7873971
X-RAY DIFFRACTIONr_scangle_it4.4634.5980
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.948 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 68 -
Rwork0.252 1397 -
obs--72.31 %

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