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- PDB-3g4a: Crystal structure of flavine dependant thymidylate synthase S88A ... -

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Basic information

Entry
Database: PDB / ID: 3g4a
TitleCrystal structure of flavine dependant thymidylate synthase S88A mutant from Thermotoga maritima at 1.95 angstrom resolution
ComponentsThymidylate synthase thyX
KeywordsTRANSFERASE / FDTS / thyX / S88A mutation / dUMP complex / FAD / Flavoprotein / Methyltransferase / Nucleotide biosynthesis
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 / 2'-DEOXYURIDINE 5'-MONOPHOSPHATE / Flavin-dependent thymidylate synthase
Similarity search - Component
Biological speciesThermotoga maritima MSB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / DIFFERENCE FOURIER / Resolution: 1.95 Å
AuthorsMathews, I.I. / Lesley, S.A. / Kohen, A.
Citation
Journal: Nature / Year: 2009
Title: An unusual mechanism of thymidylate biosynthesis in organisms containing the thyX gene.
Authors: Koehn, E.M. / Fleischmann, T. / Conrad, J.A. / Palfey, B.A. / Lesley, S.A. / Mathews, I.I. / Kohen, A.
#1: Journal: Structure / Year: 2003
Title: Functional analysis of substrate and cofactor complex structures of a thymidylate synthase-complementing protein.
Authors: Mathews, I.I. / Deacon, A.M. / Canaves, J.M. / McMullan, D. / Lesley, S.A. / Agarwalla, S. / Kuhn, P.
#2: Journal: Biochemistry / Year: 2004
Title: Mechanistic studies of a flavin-dependent thymidylate synthase.
Authors: Agrawal, N. / Lesley, S.A. / Kuhn, P. / Kohen, A.
History
DepositionFeb 3, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 7, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / 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
Revision 1.3Feb 1, 2023Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)114,32612
Polymers109,9514
Non-polymers4,3758
Water2,864159
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13490 Å2
ΔGint-55.8 kcal/mol
Surface area33980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.952, 116.222, 140.728
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1115A1 - 220
2115B1 - 220
3115C1 - 220
4115D1 - 220

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Components

#1: Protein
Thymidylate synthase thyX / TS / TSase


Mass: 27487.680 Da / Num. of mol.: 4 / Mutation: S88A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima MSB8 (bacteria) / Strain: MSB8 / DSM 3109 / JCM 10099 / Gene: thy1, thyX, TM_0449 / Plasmid: MH1 / Production host: Escherichia coli (E. coli) / Strain (production host): DL41 / References: UniProt: Q9WYT0, thymidylate synthase (FAD)
#2: Chemical
ChemComp-UMP / 2'-DEOXYURIDINE 5'-MONOPHOSPHATE / DUMP


Mass: 308.182 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H13N2O8P
#3: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 159 / 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: 2.01 Å3/Da / Density % sol: 38.7 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 42% PEG 200, 0.1M 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: 0.9795 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Mar 1, 2007 / Details: Flat collimating mirror, toroid focusing mirror
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.95→89.4 Å / Num. all: 65136 / Num. obs: 65136 / % possible obs: 99.6 % / Redundancy: 4.4 % / Rsym value: 0.066 / Net I/σ(I): 13.2
Reflection shellResolution: 1.95→2 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 1.5 / Num. unique all: 4580 / Rsym value: 0.692 / % possible all: 99.6

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Processing

Software
NameVersionClassification
Blu-Icedata collection
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
REFMAC5.2.0019phasing
RefinementMethod to determine structure: DIFFERENCE FOURIER / Resolution: 1.95→89.4 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.953 / SU B: 7.881 / SU ML: 0.117 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.179 / ESU R Free: 0.153 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22173 3288 5.1 %RANDOM
Rwork0.18565 ---
obs0.18746 61778 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.475 Å2
Baniso -1Baniso -2Baniso -3
1-3.1 Å20 Å20 Å2
2---0.71 Å20 Å2
3----2.39 Å2
Refinement stepCycle: LAST / Resolution: 1.95→89.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7042 0 292 159 7493
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0227552
X-RAY DIFFRACTIONr_bond_other_d0.0020.025118
X-RAY DIFFRACTIONr_angle_refined_deg1.5881.99310282
X-RAY DIFFRACTIONr_angle_other_deg0.958312352
X-RAY DIFFRACTIONr_dihedral_angle_1_deg65858
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.64922.259332
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.439151221
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5721555
X-RAY DIFFRACTIONr_chiral_restr0.090.21090
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.028097
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021690
X-RAY DIFFRACTIONr_nbd_refined0.210.21567
X-RAY DIFFRACTIONr_nbd_other0.2080.25529
X-RAY DIFFRACTIONr_nbtor_refined0.1920.23693
X-RAY DIFFRACTIONr_nbtor_other0.090.23732
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1580.2254
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1980.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2390.248
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2040.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7951.54432
X-RAY DIFFRACTIONr_mcbond_other0.2221.51722
X-RAY DIFFRACTIONr_mcangle_it1.21126984
X-RAY DIFFRACTIONr_scbond_it1.76733985
X-RAY DIFFRACTIONr_scangle_it2.6374.53298
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1225medium positional0.350.5
2B1225medium positional0.380.5
3C1225medium positional0.390.5
4D1225medium positional0.370.5
1A1613loose positional0.645
2B1613loose positional0.565
3C1613loose positional0.675
4D1613loose positional0.65
1A1225medium thermal0.722
2B1225medium thermal0.762
3C1225medium thermal0.742
4D1225medium thermal0.822
1A1613loose thermal1.5410
2B1613loose thermal1.410
3C1613loose thermal1.3810
4D1613loose thermal1.6510
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 248 -
Rwork0.246 4330 -
obs--95.61 %
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)
10.28340.06290.1620.57060.27811.75380.0019-0.04320.0402-0.0674-0.00780.022-0.2219-0.20240.0059-0.03340.0108-0.0121-0.01770.005-0.066327.78260.178121.875
20.7450.34960.24361.03990.54951.38830.02750.0423-0.0126-0.21060.0549-0.1881-0.14690.1322-0.0824-0.0631-0.02240.0438-0.01610.0094-0.038943.93845.13697.579
30.4946-0.0772-0.49360.78310.29881.6265-0.0090.046-0.0973-0.04220.00710.01990.1809-0.12660.0019-0.1013-0.0282-0.0125-0.0263-0.0037-0.017725.18628.268104.98
40.3728-0.0794-0.04231.16280.8171.66610.0169-0.0755-0.11380.21170.0823-0.1130.16990.1026-0.0992-0.06820.0015-0.04080.00840.0282-0.052540.26140.333133.315
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 216
2X-RAY DIFFRACTION2B0 - 219
3X-RAY DIFFRACTION3C1 - 218
4X-RAY DIFFRACTION4D1 - 218

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