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- PDB-4gt9: T. Maritima FDTS with FAD, dUMP and Folate. -

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Basic information

Entry
Database: PDB / ID: 4gt9
TitleT. Maritima FDTS with FAD, dUMP and Folate.
ComponentsThymidylate synthase thyX
KeywordsTRANSFERASE / Flavin-dependent thymidylate synthase / TM0449 / FAD / dUMP / 5 / 10-Methylenetetrahydrofolate
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 / DI(HYDROXYETHYL)ETHER / 2'-DEOXYURIDINE 5'-MONOPHOSPHATE / Flavin-dependent thymidylate synthase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.39 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)29,6547
Polymers27,5041
Non-polymers2,1506
Water3,747208
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)118,61528
Polymers110,0154
Non-polymers8,60124
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 area25500 Å2
ΔGint-68 kcal/mol
Surface area31050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.320, 110.320, 120.570
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-462-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Thymidylate synthase thyX / TS / TSase


Mass: 27503.680 Da / Num. of mol.: 1
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 , 6 types, 214 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.: 2 / Source method: obtained synthetically / Formula: C20H23N7O6
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 208 / 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: 3.33 Å3/Da / Density % sol: 63.11 %
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: Mar 11, 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: 1.39→40 Å / Num. all: 74209 / Num. obs: 74209 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.4 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 27.7
Reflection shellResolution: 1.39→1.43 Å / Redundancy: 8.4 % / Rmerge(I) obs: 0.876 / Mean I/σ(I) obs: 2.7 / Num. unique all: 5446 / % possible all: 99.9

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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 ENTRY 1O26

1o26


Resolution: 1.39→27.58 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.974 / SU B: 1.144 / SU ML: 0.025 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.041 / ESU R Free: 0.041 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16416 3736 5 %RANDOM
Rwork0.15237 ---
obs0.15295 70453 99.65 %-
all-70453 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 18.262 Å2
Baniso -1Baniso -2Baniso -3
1--0.31 Å20 Å20 Å2
2---0.31 Å20 Å2
3---0.62 Å2
Refinement stepCycle: LAST / Resolution: 1.39→27.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1786 0 126 208 2120
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222037
X-RAY DIFFRACTIONr_bond_other_d0.0020.021403
X-RAY DIFFRACTIONr_angle_refined_deg1.7562.0232782
X-RAY DIFFRACTIONr_angle_other_deg0.95233378
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0545228
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.80222.02194
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.56615336
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.4311519
X-RAY DIFFRACTIONr_chiral_restr0.1390.2290
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022191
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02462
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_it0.8741.51117
X-RAY DIFFRACTIONr_mcbond_other0.2481.5440
X-RAY DIFFRACTIONr_mcangle_it1.68721820
X-RAY DIFFRACTIONr_scbond_it2.4193920
X-RAY DIFFRACTIONr_scangle_it3.8154.5960
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.39→1.426 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.231 271 -
Rwork0.232 5164 -
obs-5164 99.91 %
Refinement TLS params.Method: refined / Origin x: -39.0345 Å / Origin y: -5.0026 Å / Origin z: 19.5295 Å
111213212223313233
T0.02 Å2-0.0052 Å20.0135 Å2-0.0478 Å20.0014 Å2--0.004 Å2
L0.9749 °2-0.5921 °20.1051 °2-1.4728 °2-0.236 °2--0.5574 °2
S0.0486 Å °0.1557 Å °0.1098 Å °-0.1092 Å °-0.0559 Å °-0.1463 Å °-0.0206 Å °0.0716 Å °0.0073 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 34
2X-RAY DIFFRACTION1A38 - 216

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