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- PDB-3n3y: Crystal structure of Thymidylate Synthase X (ThyX) from Helicobac... -

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Basic information

Entry
Database: PDB / ID: 3n3y
TitleCrystal structure of Thymidylate Synthase X (ThyX) from Helicobacter pylori with FAD and dUMP at 2.31A resolution
ComponentsThymidylate synthase thyX
KeywordsTRANSFERASE / Thymidylate synthase ThyX / Helicobacter pylori
Function / homology
Function and homology information


thymidylate synthase (FAD) / thymidylate synthase (FAD) activity / dTMP biosynthetic process / dTTP biosynthetic process / 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 speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.307 Å
AuthorsWang, K. / Wang, Q. / Chen, J. / Chen, L. / Jiang, H. / Shen, X.
CitationJournal: To be Published
Title: Structure, Enzymatic Characterization and Inhibitor Discovery of Thymidylate Synthase X (ThyX) from Helicobacter pylori Strain SS1
Authors: Wang, K. / Wang, Q. / Chen, J. / Chen, L. / Jiang, H. / Shen, X.
History
DepositionMay 21, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 25, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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

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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)104,17313
Polymers99,4894
Non-polymers4,6839
Water2,648147
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14070 Å2
ΔGint-46 kcal/mol
Surface area33520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.525, 79.956, 96.405
Angle α, β, γ (deg.)90.000, 103.140, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Thymidylate synthase thyX / Thymidylate Synthase X / thyX / TS / TSase


Mass: 24872.373 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: SS1 / Gene: ThyX / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5UVJ4, thymidylate synthase (FAD)
#2: Chemical
ChemComp-UMP / 2'-DEOXYURIDINE 5'-MONOPHOSPHATE / DUMP / Deoxyuridine monophosphate


Mass: 308.182 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C9H13N2O8P
#3: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / 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 / Water


Mass: 18.015 Da / Num. of mol.: 147 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.47 Å3/Da / Density % sol: 50.24 % / Mosaicity: 0.602 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.2M Sodium chloride, 0.1M MES pH 6.0, 20%(w/v) PEG 2000 MME, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRF BL17U10.9794
SYNCHROTRONSSRF BL17U20.9794, 0.9796, 0.9719
Detector
TypeIDDetector
MARMOSAIC 225 mm CCD1CCD
MARMOSAIC 225 mm CCD2CCD
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97941
20.97961
30.97191
ReflectionResolution: 2.307→50 Å / Num. obs: 42568 / % possible obs: 99.6 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.063 / Χ2: 1.602 / Net I/σ(I): 14.3
Reflection shellResolution: 2.307→2.39 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.318 / Num. unique all: 4166 / Χ2: 1.126 / % possible all: 98.4

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.5_2refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.307→37.687 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.833 / SU ML: 0.3 / σ(F): 1.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.223 2144 5.04 %
Rwork0.174 --
obs0.176 42533 99.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.238 Å2 / ksol: 0.367 e/Å3
Displacement parametersBiso max: 116.58 Å2 / Biso mean: 43.844 Å2 / Biso min: 19.39 Å2
Baniso -1Baniso -2Baniso -3
1-8.737 Å20 Å27.878 Å2
2--1.231 Å2-0 Å2
3----9.968 Å2
Refinement stepCycle: LAST / Resolution: 2.307→37.687 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6793 0 312 147 7252
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077260
X-RAY DIFFRACTIONf_angle_d1.1119836
X-RAY DIFFRACTIONf_chiral_restr0.0721078
X-RAY DIFFRACTIONf_plane_restr0.0041209
X-RAY DIFFRACTIONf_dihedral_angle_d19.7672710
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.307-2.390.2872040.2073856406096
2.39-2.4860.2991800.240564236100
2.486-2.5990.262170.19540454262100
2.599-2.7360.2731980.18440814279100
2.736-2.9070.2612250.20440144239100
2.907-3.1310.2732460.19940474293100
3.131-3.4460.2232190.17240814300100
3.446-3.9440.22310.15640204251100
3.944-4.9680.1722070.13940884295100
4.968-37.6920.1982170.1744101431898

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