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- PDB-4gtf: T. Maritima FDTS (H53A mutant) with FAD, dUMP and Folate -

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Basic information

Entry
Database: PDB / ID: 4gtf
TitleT. Maritima FDTS (H53A mutant) with FAD, dUMP and Folate
ComponentsThymidylate synthase thyX
KeywordsTRANSFERASE / Flavin-dependent thymidylate synthase / TM0449 / H53A mutant / FAD / 5 / 10-Methylenetetrahydrofolate / dUMP
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 / 2'-DEOXYURIDINE 5'-MONOPHOSPHATE / Flavin-dependent thymidylate synthase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å
AuthorsMathews, I.I. / Lesley, S.A. / Kohen, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0235
Polymers27,4371
Non-polymers1,5874
Water2,234124
1
A: Thymidylate synthase thyX
hetero molecules

A: Thymidylate synthase thyX
hetero molecules

A: Thymidylate synthase thyX
hetero molecules

A: Thymidylate synthase thyX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,09320
Polymers109,7464
Non-polymers6,34716
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_455y-1/2,x+1/2,-z+1/21
crystal symmetry operation10_455-x-1,-y,z1
crystal symmetry operation16_445-y-1/2,-x-1/2,-z+1/21
Buried area14980 Å2
ΔGint-58 kcal/mol
Surface area33640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.810, 109.810, 122.290
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-508-

HOH

21A-509-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Thymidylate synthase thyX / TS / TSase


Mass: 27436.611 Da / Num. of mol.: 1 / Mutation: H53A
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)

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Non-polymers , 5 types, 128 molecules

#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-UMP / 2'-DEOXYURIDINE 5'-MONOPHOSPHATE / DUMP


Mass: 308.182 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H13N2O8P
#4: 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.: 1 / Source method: obtained synthetically / Formula: C20H23N7O6
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / 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: 3.36 Å3/Da / Density % sol: 63.38 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.58
Details: 3-6% PEG 4K (w/v), 200mM NaCl, 100 mM Na/K phosphate (pH 6.58), 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: Feb 27, 2011 / 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: 1.77→40 Å / Num. all: 36610 / Num. obs: 36610 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.1 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 23.3
Reflection shellResolution: 1.77→1.82 Å / Redundancy: 9.2 % / Rmerge(I) obs: 0.969 / Mean I/σ(I) obs: 2.7 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-Icedata collection
MOLREPphasing
REFMAC5.5.0110refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Code: 1O26

1o26


Resolution: 1.77→38.82 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.969 / SU B: 3.04 / SU ML: 0.053 / Cross valid method: THROUGHOUT / ESU R: 0.082 / ESU R Free: 0.079 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17812 1830 5 %RANDOM
Rwork0.16185 ---
obs0.16266 34764 99.93 %-
all-34763 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 30.244 Å2
Baniso -1Baniso -2Baniso -3
1--0.71 Å20 Å20 Å2
2---0.71 Å20 Å2
3---1.42 Å2
Refinement stepCycle: LAST / Resolution: 1.77→38.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1782 0 98 124 2004
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0192022
X-RAY DIFFRACTIONr_bond_other_d0.0020.021401
X-RAY DIFFRACTIONr_angle_refined_deg1.7232.0082754
X-RAY DIFFRACTIONr_angle_other_deg0.93433366
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0385226
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.52522.06297
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.91215337
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4131520
X-RAY DIFFRACTIONr_chiral_restr0.1230.2289
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022173
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02467
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_it0.8621.51119
X-RAY DIFFRACTIONr_mcbond_other0.2551.5443
X-RAY DIFFRACTIONr_mcangle_it1.67521817
X-RAY DIFFRACTIONr_scbond_it2.5743901
X-RAY DIFFRACTIONr_scangle_it4.1554.5930
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.77→1.816 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.23 109 -
Rwork0.22 2334 -
obs--99.88 %
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)
12.5722-2.64070.14173.02770.01170.47950.36350.50650.0992-0.4981-0.3588-0.0766-0.0550.0235-0.00470.13030.02090.02860.20260.04610.0271-46.77312.832511.8606
21.487-0.94930.14682.57-0.32630.89590.07660.1730.1491-0.12-0.0857-0.2884-0.02840.11920.00910.0274-0.00430.01920.06090.00390.037-37.5044-6.027921.4773
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 33
2X-RAY DIFFRACTION2A36 - 215

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