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- PDB-4gte: T. Maritima FDTS (E144R mutant) with FAD and Folate -

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Basic information

Entry
Database: PDB / ID: 4gte
TitleT. Maritima FDTS (E144R mutant) with FAD and Folate
ComponentsThymidylate synthase thyX
KeywordsTRANSFERASE / Flavin-dependent thymidylate synthase / TM0449 / E144R mutant / Folate
Function / homology
Function and homology information


thymidylate synthase (FAD) / thymidylate synthase (FAD) activity / thymidylate synthase activity / dTMP biosynthetic process / dTTP biosynthetic process / NADPH binding / flavin adenine dinucleotide binding / methylation
Similarity search - Function
Gyrase A; domain 2 - #170 / Thymidylate synthase ThyX / Thymidylate synthase ThyX superfamily / Thymidylate synthase complementing protein / Flavin-dependent thymidylate synthase (thyX) domain profile. / Gyrase A; domain 2 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Chem-MEF / Flavin-dependent thymidylate synthase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.89 Å
AuthorsMathews, I.I. / Lesley, S.A. / Kohen, A. / Prabhakar, A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Folate binding site of flavin-dependent thymidylate synthase.
Authors: Koehn, E.M. / Perissinotti, L.L. / Moghram, S. / Prabhakar, A. / Lesley, S.A. / Mathews, I.I. / Kohen, A.
History
DepositionAug 28, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 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 thyX
B: Thymidylate synthase thyX
C: Thymidylate synthase thyX
D: Thymidylate synthase thyX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,18410
Polymers110,1274
Non-polymers4,0576
Water2,918162
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21120 Å2
ΔGint-74 kcal/mol
Surface area33350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.710, 117.070, 141.910
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Thymidylate synthase thyX / TS / TSase


Mass: 27531.760 Da / Num. of mol.: 4 / Mutation: E144R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 / Gene: thyX, thy1, TM_0449 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9WYT0, thymidylate synthase (FAD)
#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-MEF / N-({4-[(6aR)-3-amino-1-oxo-1,2,5,6,6a,7-hexahydroimidazo[1,5-f]pteridin-8(9H)-yl]phenyl}carbonyl)-L-glutamic acid / 5,10-methylene,5,6,7,8-tetrahydrofolate


Mass: 457.440 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H23N7O6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 162 / 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: 2.06 Å3/Da / Density % sol: 40.39 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 50-60% PEG 200 and 100mM Tris HCL (pH 8.0), VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 28, 2011 / Details: K-B focusing mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.89→40 Å / Num. all: 73284 / Num. obs: 73284 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 14.5
Reflection shellResolution: 1.89→1.94 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.97 / Mean I/σ(I) obs: 1.7 / Num. unique all: 5349 / % possible all: 99.4

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Processing

Software
NameVersionClassification
Blu-Icedata collection
REFMAC5.5.0110refinement
XDSdata reduction
XDSdata scaling
REFMAC5.5.0110phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1O26

1o26


Resolution: 1.89→38.47 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.954 / SU B: 7.007 / SU ML: 0.099 / Cross valid method: THROUGHOUT / σ(I): 0 / ESU R: 0.157 / ESU R Free: 0.136 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21266 3687 5 %RANDOM
Rwork0.18367 ---
obs0.18512 69504 99.17 %-
all-69504 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 33.883 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20 Å20 Å2
2---0.05 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.89→38.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7231 0 206 162 7599
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0227674
X-RAY DIFFRACTIONr_bond_other_d0.0010.025341
X-RAY DIFFRACTIONr_angle_refined_deg1.6661.97910414
X-RAY DIFFRACTIONr_angle_other_deg0.978312839
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1075855
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.68822.277382
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.891151307
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8791572
X-RAY DIFFRACTIONr_chiral_restr0.1090.21106
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0218256
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021748
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_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9231.54312
X-RAY DIFFRACTIONr_mcbond_other0.2861.51711
X-RAY DIFFRACTIONr_mcangle_it1.66227001
X-RAY DIFFRACTIONr_scbond_it2.62833362
X-RAY DIFFRACTIONr_scangle_it4.2174.53412
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.89→1.939 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 270 -
Rwork0.266 5055 -
obs--99.35 %
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)
11.00220.06220.57841.25660.9214.82540.0136-0.00840.05950.0552-0.02950.0419-0.2059-0.27580.0160.04730.0053-0.00720.02170.01580.077328.409560.9694123.0666
21.12110.56170.44992.87731.68273.24210.01530.0587-0.04-0.26990.0672-0.3099-0.02730.1904-0.08240.04120.00520.04220.04710.04410.102844.565245.272797.4661
30.9317-0.15-0.90141.57270.98394.27730.01630.0504-0.0771-0.1214-0.00930.05470.1012-0.2411-0.0070.0211-0.0116-0.01860.01640.01370.11425.598328.2148106.1904
40.9802-0.626-0.65332.96171.99753.2421-0.0408-0.1348-0.03050.3240.156-0.25530.12070.3048-0.11520.0637-0.0057-0.05050.07580.04610.086940.916140.1816133.8459
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 33
2X-RAY DIFFRACTION1A38 - 217
3X-RAY DIFFRACTION2B0 - 31
4X-RAY DIFFRACTION2B37 - 91
5X-RAY DIFFRACTION2B94 - 220
6X-RAY DIFFRACTION3C1 - 32
7X-RAY DIFFRACTION3C36 - 220
8X-RAY DIFFRACTION4D1 - 32
9X-RAY DIFFRACTION4D37 - 218

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