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- PDB-5iot: Flavin-dependent thymidylate synthase R174A variant in complex wi... -

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Basic information

Entry
Database: PDB / ID: 5iot
TitleFlavin-dependent thymidylate synthase R174A variant in complex with FAD and dUMP
ComponentsThymidylate synthase ThyX
KeywordsTRANSFERASE / FAD-dependent / nucleotide biosynthesis / reductive methylation
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 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsBernard, S.M. / Stull, F.W. / Smith, J.L.
Funding support United States, 3items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE 1213620 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)R01DK042303 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM081544 United States
CitationJournal: Biochemistry / Year: 2016
Title: Deprotonations in the Reaction of Flavin-Dependent Thymidylate Synthase.
Authors: Stull, F.W. / Bernard, S.M. / Sapra, A. / Smith, J.L. / Zuiderweg, E.R. / Palfey, B.A.
History
DepositionMar 8, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 8, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 22, 2016Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_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)114,04512
Polymers109,6704
Non-polymers4,3758
Water4,738263
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23000 Å2
ΔGint-71 kcal/mol
Surface area31010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.060, 115.860, 141.100
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
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: MET / Beg label comp-ID: MET / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSAA1 - 21613 - 228
21LYSLYSBB1 - 21613 - 228
12GLUGLUAA1 - 21713 - 229
22GLUGLUCC1 - 21713 - 229
13VALVALAA1 - 21813 - 230
23VALVALDD1 - 21813 - 230
14LYSLYSBB1 - 21613 - 228
24LYSLYSCC1 - 21613 - 228
15LEULEUBB1 - 21513 - 227
25LEULEUDD1 - 21513 - 227
16VALVALCC1 - 21813 - 230
26VALVALDD1 - 21813 - 230

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Thymidylate synthase ThyX / TSase


Mass: 27417.564 Da / Num. of mol.: 4 / Mutation: R174A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099) (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-UMP / 2'-DEOXYURIDINE 5'-MONOPHOSPHATE / DUMP


Mass: 308.182 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H13N2O8P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 263 / 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: 38.95 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion / pH: 8
Details: 40-50% PEG 200, 0-150 mM NaCl, 100 mM Tris-HCl pH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 14, 2013
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2→89.54 Å / Num. obs: 54863 / % possible obs: 90.7 % / Redundancy: 6 % / Net I/σ(I): 8.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0069refinement
iMOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GT9

4gt9


Resolution: 2→89.54 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.945 / SU B: 4.938 / SU ML: 0.133 / Cross valid method: THROUGHOUT / ESU R: 0.233 / ESU R Free: 0.177 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21742 2753 5 %RANDOM
Rwork0.18277 ---
obs0.1845 52046 90.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 34.545 Å2
Baniso -1Baniso -2Baniso -3
1--0.78 Å20 Å20 Å2
2--1.9 Å2-0 Å2
3----1.12 Å2
Refinement stepCycle: 1 / Resolution: 2→89.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7168 0 292 263 7723
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0197695
X-RAY DIFFRACTIONr_bond_other_d0.0050.027210
X-RAY DIFFRACTIONr_angle_refined_deg1.4891.99510466
X-RAY DIFFRACTIONr_angle_other_deg1.198316540
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9325861
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.45822.486366
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.523151279
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7371564
X-RAY DIFFRACTIONr_chiral_restr0.0860.21109
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0218347
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021887
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_it1.9553.2293456
X-RAY DIFFRACTIONr_mcbond_other1.9553.2293455
X-RAY DIFFRACTIONr_mcangle_it2.8414.8284313
X-RAY DIFFRACTIONr_mcangle_other2.8414.8294314
X-RAY DIFFRACTIONr_scbond_it2.7063.5334239
X-RAY DIFFRACTIONr_scbond_other2.7063.5334240
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.2995.1516154
X-RAY DIFFRACTIONr_long_range_B_refined5.81226.7489429
X-RAY DIFFRACTIONr_long_range_B_other5.77726.6719346
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A131570.1
12B131570.1
21A132440.1
22C132440.1
31A131840.1
32D131840.1
41B131240.11
42C131240.11
51B135170.1
52D135170.1
61C131770.11
62D131770.11
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 176 -
Rwork0.263 3598 -
obs--85.97 %

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