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- PDB-5ior: Flavin-dependent thymidylate synthase in complex with FAD and 2'-... -

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Basic information

Entry
Database: PDB / ID: 5ior
TitleFlavin-dependent thymidylate synthase in complex with FAD and 2'-deoxyuridine-5'-monosulfate
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
2'-deoxy-5'-O-sulfouridine / FLAVIN-ADENINE DINUCLEOTIDE / RIBOFLAVIN / Flavin-dependent thymidylate synthase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thymidylate synthase ThyX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9744
Polymers27,5041
Non-polymers1,4703
Water1,76598
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)115,89516
Polymers110,0154
Non-polymers5,88112
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z1
crystal symmetry operation10_555-x,-y,z1
crystal symmetry operation15_555y,x,-z1
Buried area24390 Å2
ΔGint-71 kcal/mol
Surface area30970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.679, 109.679, 119.864
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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Components

#1: Protein Thymidylate synthase ThyX / TSase


Mass: 27503.680 Da / Num. of mol.: 1
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.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-DUS / 2'-deoxy-5'-O-sulfouridine / 2'-deoxyuridine-5'-monosulfate


Mass: 308.265 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H12N2O8S
#4: Chemical ChemComp-RBF / RIBOFLAVIN / RIBOFLAVINE / VITAMIN B2


Mass: 376.364 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H20N4O6
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / 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: 3.28 Å3/Da / Density % sol: 62.46 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion / pH: 6.6
Details: 7% PEG 4K, 100 mM NaCl, 100 mM Na/K phosphate, pH 6.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 7, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.95→80.92 Å / Num. obs: 27043 / % possible obs: 99.7 % / Redundancy: 14.6 % / Net I/σ(I): 20.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GT9

4gt9


Resolution: 1.95→80.92 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.957 / SU B: 4.761 / SU ML: 0.074 / Cross valid method: THROUGHOUT / ESU R: 0.109 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19148 1270 4.7 %RANDOM
Rwork0.16204 ---
obs0.16341 25671 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.196 Å2
Baniso -1Baniso -2Baniso -3
1--0.99 Å20 Å2-0 Å2
2---0.99 Å20 Å2
3---1.97 Å2
Refinement stepCycle: LAST / Resolution: 1.95→80.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1801 0 100 98 1999
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0191988
X-RAY DIFFRACTIONr_bond_other_d0.0010.021844
X-RAY DIFFRACTIONr_angle_refined_deg1.3421.9942711
X-RAY DIFFRACTIONr_angle_other_deg0.78634234
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0175222
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.31322.39696
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.05515327
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2411518
X-RAY DIFFRACTIONr_chiral_restr0.0820.2285
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022195
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02488
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_it1.122.205877
X-RAY DIFFRACTIONr_mcbond_other1.122.205877
X-RAY DIFFRACTIONr_mcangle_it1.7423.2931096
X-RAY DIFFRACTIONr_mcangle_other1.7413.2931097
X-RAY DIFFRACTIONr_scbond_it1.7472.531111
X-RAY DIFFRACTIONr_scbond_other1.7342.531111
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.8443.7181614
X-RAY DIFFRACTIONr_long_range_B_refined5.04121.7582537
X-RAY DIFFRACTIONr_long_range_B_other4.98621.6072510
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.234 92 -
Rwork0.234 1887 -
obs--100 %
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)
15.2276-0.99331.89695.71094.79096.12330.1549-0.0251-0.0511-0.4159-0.0623-0.0688-0.00480.0199-0.09260.18190.0309-0.00910.04960.02810.02237.600319.2588-21.6735
22.59982.57350.25513.58760.94950.6196-0.22310.3431-0.1018-0.3440.2797-0.1342-0.09250.0535-0.05660.085-0.0148-0.00210.10540.00840.04392.988212.1588-18.6321
32.7133-0.65741.34477.02781.22112.24090.0290.24280.1946-0.3814-0.04690.4277-0.0978-0.16930.01790.0718-0.01-0.02210.15520.03630.1232-18.56813.2794-16.9654
41.12950.51980.01690.7845-0.01510.6217-0.00590.0210.1308-0.05520.0104-0.0143-0.12620.0494-0.00440.04910.00060.00910.04140.01140.03429.921316.2387-8.142
54.357-5.1672-0.69956.49091.12220.91370.1360.05370.3516-0.3174-0.0285-0.3225-0.24450.0327-0.10750.1088-0.03110.01530.07840.01010.109326.491827.7291-4.6647
61.10050.37120.13890.43070.23210.3082-0.02860.02620.0736-0.05790.02030.0367-0.05890.0020.00830.02740.00310.00580.01470.01550.0277.213816.5511-7.2913
73.01320.39160.09734.02382.63536.0195-0.05010.08980.3165-0.26770.00380.2062-0.3368-0.0420.04630.0690.0083-0.04380.06240.0590.1132-9.717.3754-14.7031
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 4
2X-RAY DIFFRACTION2A5 - 23
3X-RAY DIFFRACTION3A24 - 54
4X-RAY DIFFRACTION4A55 - 110
5X-RAY DIFFRACTION5A111 - 143
6X-RAY DIFFRACTION6A144 - 191
7X-RAY DIFFRACTION7A192 - 218

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