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- PDB-5jfe: Flavin-dependent thymidylate synthase with H2-dUMP -

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Basic information

Entry
Database: PDB / ID: 5jfe
TitleFlavin-dependent thymidylate synthase with H2-dUMP
ComponentsThymidylate synthase ThyX
KeywordsTRANSFERASE / thymidylate synthase / complex / H2-dUMP ligand
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'-deoxy-5'-uridylic acid / Flavin-dependent thymidylate synthase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.03 Å
AuthorsSapra, A. / Stuckey, J. / Palfey, B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)NSF CHE 1213620 United States
CitationJournal: To Be Published
Title: Evaluating H2-dUMP as an Intermediate in the oxidation of Flavin-dependent Thymidylate Synthase
Authors: Sapra, A. / Stuckey, J. / Palfey, B.
History
DepositionApr 19, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 26, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 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

Downloads & links

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Assembly

Deposited unit
A: Thymidylate synthase ThyX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9108
Polymers27,5041
Non-polymers1,4067
Water1,982110
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)115,63932
Polymers110,0154
Non-polymers5,62428
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_454y-1/2,x+1/2,-z-1/21
crystal symmetry operation10_565-x,-y+1,z1
crystal symmetry operation16_554-y+1/2,-x+1/2,-z-1/21
Buried area25060 Å2
ΔGint-8 kcal/mol
Surface area29950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.322, 110.322, 120.765
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-510-

HOH

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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 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q9WYT0, thymidylate synthase (FAD)
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-UMC / 2'-deoxy-5'-uridylic acid


Mass: 310.198 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H15N2O8P
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 110 / 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: 3.34 Å3/Da / Density % sol: 63.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.6
Details: 1- 6% PEG 4000, 0-30 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: 21-ID-F / Wavelength: 0.9787 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 11, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 2.03→50 Å / Num. obs: 24294 / % possible obs: 100 % / Redundancy: 17.1 % / Biso Wilson estimate: 24.77 Å2 / Rmerge(I) obs: 0.089 / Rpim(I) all: 0.022 / Rrim(I) all: 0.092 / Χ2: 1.08 / Net I/av σ(I): 41.273 / Net I/σ(I): 8.2 / Num. measured all: 415659
Reflection shell

Diffraction-ID: 1 / Rejects: 0 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2
2.03-2.0717.30.41611940.9780.1020.4290.706
2.07-2.117.30.36512000.9820.090.3760.716
2.1-2.1417.40.32912030.9870.0810.3390.708
2.14-2.1917.40.30411790.9880.0740.3130.734
2.19-2.2317.30.25712000.990.0630.2650.737
2.23-2.2917.40.23212000.9920.0570.2390.756
2.29-2.3417.40.212040.9950.0490.2060.775
2.34-2.4117.30.18911870.9950.0460.1950.766
2.41-2.4817.40.16611930.9950.0410.1710.792
2.48-2.5617.40.14912130.9970.0370.1530.807
2.56-2.6517.30.12311940.9970.030.1270.84
2.65-2.7617.40.1112120.9980.0270.1140.864
2.76-2.8817.30.09912230.9990.0240.1020.886
2.88-3.0317.30.08711920.9980.0210.090.976
3.03-3.2217.30.07212130.9990.0180.0741.235
3.22-3.4717.10.07212250.9990.0180.0741.756
3.47-3.8216.70.0712290.9980.0180.0722.295
3.82-4.3716.50.06312310.9990.0160.0652.596
4.37-5.5116.40.04712670.9990.0120.0481.594
5.51-5015.60.036133510.0090.0371.129

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
BUSTER-TNT2.10.2refinement
HKL-2000data scaling
MOLREPphasing
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GTE

4gte


Resolution: 2.03→47.75 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.93 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.126 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.129 / SU Rfree Blow DPI: 0.114 / SU Rfree Cruickshank DPI: 0.113
RfactorNum. reflection% reflectionSelection details
Rfree0.19 1224 5.04 %RANDOM
Rwork0.17 ---
obs0.171 24280 99.6 %-
Displacement parametersBiso max: 102.67 Å2 / Biso mean: 27.03 Å2 / Biso min: 10.22 Å2
Baniso -1Baniso -2Baniso -3
1-3.4812 Å20 Å20 Å2
2--3.4812 Å20 Å2
3----6.9624 Å2
Refine analyzeLuzzati coordinate error obs: 0.21 Å
Refinement stepCycle: final / Resolution: 2.03→47.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1771 0 93 110 1974
Biso mean--26.38 35.66 -
Num. residues----213
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d954SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes40HARMONIC2
X-RAY DIFFRACTIONt_gen_planes338HARMONIC5
X-RAY DIFFRACTIONt_it2048HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion258SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2598SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2048HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg2780HARMONIC20.93
X-RAY DIFFRACTIONt_omega_torsion3.56
X-RAY DIFFRACTIONt_other_torsion2.74
LS refinement shellResolution: 2.03→2.12 Å / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.206 133 4.71 %
Rwork0.165 2689 -
all-2822 -
obs--96.34 %

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