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- PDB-1o25: Crystal structure of Thymidylate Synthase Complementing Protein (... -

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Basic information

Entry
Database: PDB / ID: 1o25
TitleCrystal structure of Thymidylate Synthase Complementing Protein (TM0449) from Thermotoga maritima with dUMP at 2.4 A resolution
ComponentsThymidylate synthase thyX
KeywordsTRANSFERASE / TM0449 / THYMIDYLATE SYNTHASE COMPLEMENTING PROTEIN / STRUCTURAL GENOMICS / JCSG / Joint Center for Structural Genomics / PSI / Protein Structure Initiative
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'-DEOXYURIDINE 5'-MONOPHOSPHATE / Flavin-dependent thymidylate synthase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement / Resolution: 2.4 Å
AuthorsMathews, I.I. / Deacon, A.M. / Canaves, J.M. / McMullan, D. / Lesley, S.A. / Agarwalla, S. / Kuhn, P. / Joint Center for Structural Genomics (JCSG)
CitationJournal: Structure / Year: 2003
Title: Functional Analysis of Substrate and Cofactor Complex Structures of a Thymidylate Synthase-Complementing Protein
Authors: Mathews, I.I. / Deacon, A.M. / Canaves, J.M. / McMullan, D. / Lesley, S.A. / Agarwalla, S. / Kuhn, P.
History
DepositionFeb 20, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Jul 18, 2018Group: Data collection / Database references / Category: pdbx_database_related
Revision 1.5Jan 25, 2023Group: Database references / Derived calculations / Category: 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
Revision 1.6Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)111,2478
Polymers110,0154
Non-polymers1,2334
Water4,053225
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16980 Å2
ΔGint-64 kcal/mol
Surface area34160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.682, 116.703, 141.727
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Thymidylate synthase thyX / TS / TSase / thymidylate synthase complementing protein


Mass: 27503.680 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM0449 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9WYT0, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Chemical
ChemComp-UMP / 2'-DEOXYURIDINE 5'-MONOPHOSPHATE / DUMP


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


Mass: 18.015 Da / Num. of mol.: 225 / 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: 2.15 Å3/Da / Density % sol: 42.45 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 49% PEG 200, 0.1M Tris-Hcl, pH 8.0, VAPOR DIFFUSION,HANGING DROP, temperature 295K
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, sitting drop / Details: Kuhn, P., (2002) Proteins, 49, 142.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
1100 mMTris-HCl1reservoirpH8.0
249 %(w/v)PEG2001reservoiror 100mM HEPES, pH7.5
344 %PEG2001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.98039
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 15, 2002
Details: Flat mirror,single crystal Si(311) bent monochromator
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98039 Å / Relative weight: 1
ReflectionResolution: 2.4→53.957 Å / Num. all: 33587 / Num. obs: 33587 / % possible obs: 93 % / Redundancy: 4 % / Biso Wilson estimate: 39.577 Å2 / Rsym value: 0.091 / Net I/σ(I): 14.1
Reflection shellResolution: 2.4→2.46 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 2.9 / Num. unique all: 2245 / Rsym value: 0.338 / % possible all: 85.6
Reflection
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 54.4 Å / Num. measured all: 134682 / Rmerge(I) obs: 0.091
Reflection shell
*PLUS
% possible obs: 85.6 % / Rmerge(I) obs: 0.338

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
RESOLVEmodel building
SOLVEphasing
CNSrefinement
CCP4(SCALA)data scaling
RESOLVEphasing
RefinementMethod to determine structure: molecular replacement
Starting model: 1KQ4

1kq4


Resolution: 2.4→20 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh and Huber
RfactorNum. reflection% reflection
Rfree0.2626 1644 4.5 %
Rwork0.1985 --
all-33513 -
obs-33242 91.8 %
Solvent computationSolvent model: Bulk solvent correction / Bsol: 0.349861 Å2 / ksol: 36.276 e/Å3
Displacement parametersBiso mean: 35.2 Å2
Baniso -1Baniso -2Baniso -3
1--7.113 Å20 Å20 Å2
2--5.058 Å20 Å2
3---2.055 Å2
Refine analyzeLuzzati coordinate error obs: 0.28 Å
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7191 0 80 225 7496
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.22
X-RAY DIFFRACTIONc_mcbond_it1.2661.5
X-RAY DIFFRACTIONc_scbond_it1.9692
X-RAY DIFFRACTIONc_mcangle_it2.0522
X-RAY DIFFRACTIONc_scangle_it2.9412.5
LS refinement shellResolution: 2.4→2.43 Å / Total num. of bins used: 32
RfactorNum. reflection% reflection
Rfree0.3217 53 5.567 %
Rwork0.248 899 -
Refinement
*PLUS
Rfactor Rfree: 0.263 / Rfactor Rwork: 0.199 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

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