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- PDB-4gtc: T. Maritima FDTS (E144R mutant) plus FAD -

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Basic information

Entry
Database: PDB / ID: 4gtc
TitleT. Maritima FDTS (E144R mutant) plus FAD
ComponentsThymidylate synthase thyX
KeywordsTRANSFERASE / Flavin-dependent thymidylate synthase / TM0449
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 / Flavin-dependent thymidylate synthase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Rigid Body refinement / Resolution: 1.97 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)113,2698
Polymers110,1274
Non-polymers3,1424
Water4,774265
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20650 Å2
ΔGint-76 kcal/mol
Surface area34440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.130, 117.060, 142.070
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 265 / 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: 2.04 Å3/Da / Density % sol: 39.81 %
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: BL9-2 / Wavelength: 0.9809 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 27, 2010 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9809 Å / Relative weight: 1
ReflectionResolution: 1.97→30 Å / Num. all: 63939 / Num. obs: 63939 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 16.4
Reflection shellResolution: 1.97→2.02 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.886 / Mean I/σ(I) obs: 1.6 / Num. unique all: 4737 / % possible all: 99.6

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Processing

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

1o26


Resolution: 1.97→29.26 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.941 / SU B: 9.487 / SU ML: 0.131 / Cross valid method: THROUGHOUT / σ(I): 0 / ESU R: 0.198 / ESU R Free: 0.169 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23573 3239 5.1 %RANDOM
Rwork0.19331 ---
obs0.19543 60636 98.72 %-
all-60636 --
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: 35.199 Å2
Baniso -1Baniso -2Baniso -3
1-2.43 Å20 Å20 Å2
2---0.89 Å20 Å2
3----1.54 Å2
Refinement stepCycle: LAST / Resolution: 1.97→29.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7261 0 194 265 7720
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0227669
X-RAY DIFFRACTIONr_bond_other_d0.0010.025331
X-RAY DIFFRACTIONr_angle_refined_deg1.6381.97710403
X-RAY DIFFRACTIONr_angle_other_deg0.966312811
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3795856
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.43422.283381
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.091151305
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8881571
X-RAY DIFFRACTIONr_chiral_restr0.0970.21101
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0218258
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021745
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_it0.8211.54325
X-RAY DIFFRACTIONr_mcbond_other0.2431.51719
X-RAY DIFFRACTIONr_mcangle_it1.40227013
X-RAY DIFFRACTIONr_scbond_it2.31733344
X-RAY DIFFRACTIONr_scangle_it3.5494.53390
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.97→2.021 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 252 -
Rwork0.282 4468 -
obs--99.64 %
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)
10.71340.17140.62811.23730.97815.00830.001-0.02670.04590.0549-0.03460.0636-0.2167-0.30240.03360.03950.00760.01150.02610.01210.083327.872161.2716122.9683
21.26560.73190.66912.64251.64023.5421-0.03560.0899-0.0463-0.25630.1282-0.33610.05250.2566-0.09250.05870.00380.06720.0670.02380.10544.146545.663397.552
31.1344-0.108-1.06491.74121.2014.66720.00560.0543-0.1085-0.2081-0.02110.02870.0994-0.25220.01550.0439-0.0136-0.01490.0170.01440.10624.918328.2587106.3302
40.6812-0.3472-0.38392.88392.1573.2797-0.0126-0.1071-0.07520.24350.1509-0.27210.11390.267-0.13820.0375-0.0058-0.04510.08710.04170.09440.32339.8912133.8763
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-2 - 34
2X-RAY DIFFRACTION1A37 - 217
3X-RAY DIFFRACTION2B0 - 32
4X-RAY DIFFRACTION2B37 - 89
5X-RAY DIFFRACTION2B94 - 219
6X-RAY DIFFRACTION3C0 - 32
7X-RAY DIFFRACTION3C35 - 220
8X-RAY DIFFRACTION4D0 - 32
9X-RAY DIFFRACTION4D36 - 218

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