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- PDB-1o2b: Crystal structure of Thymidylate Synthase Complementing Protein (... -

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Basic information

Entry
Database: PDB / ID: 1o2b
TitleCrystal structure of Thymidylate Synthase Complementing Protein (TM0449) from Thermotoga maritima with FAD and PO4 at 2.45 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
FLAVIN-ADENINE DINUCLEOTIDE / PHOSPHATE ION / Flavin-dependent thymidylate synthase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 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 18, 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)113,44211
Polymers110,0154
Non-polymers3,4277
Water4,324240
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21540 Å2
ΔGint-83 kcal/mol
Surface area33500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.991, 118.150, 145.400
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-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-FAD / 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


Mass: 18.015 Da / Num. of mol.: 240 / 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: 2.22 Å3/Da / Density % sol: 44.11 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 45 PEG 200, 0.1M HEPES, pH 7.5, 8mM sodium, VAPOR DIFFUSION,HANGING DROP, temperature 295K
Crystal grow
*PLUS
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: 0.94641
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Mar 24, 2002
Details: Flat mirror,single crystal Si(311) bent monochromator
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.94641 Å / Relative weight: 1
ReflectionResolution: 2.45→47.16 Å / Num. all: 33811 / Num. obs: 33811 / % possible obs: 95 % / Redundancy: 2.9 % / Biso Wilson estimate: 46.811 Å2 / Rsym value: 0.081 / Net I/σ(I): 10.1
Reflection shellResolution: 2.45→2.51 Å / Redundancy: 2.1 % / Mean I/σ(I) obs: 1.4 / Num. unique all: 2015 / Rsym value: 0.66 / % possible all: 77.9
Reflection
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 47.1 Å / Num. obs: 32278 / % possible obs: 96.2 % / Num. measured all: 96569 / Rmerge(I) obs: 0.08
Reflection shell
*PLUS
% possible obs: 87.3 % / Rmerge(I) obs: 0.469

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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: 2.45→20 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh and Huber
RfactorNum. reflection% reflection
Rfree0.265 1639 4.6 %
Rwork0.2027 --
all-33734 -
obs-33130 93 %
Solvent computationSolvent model: Bulk solvent correction / Bsol: 0.348113 Å2 / ksol: 52.0584 e/Å3
Displacement parametersBiso mean: 50.9 Å2
Baniso -1Baniso -2Baniso -3
1--9.447 Å20 Å20 Å2
2--6.085 Å20 Å2
3---3.362 Å2
Refine analyzeLuzzati coordinate error obs: 0.3118 Å
Refinement stepCycle: LAST / Resolution: 2.45→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7136 0 227 240 7603
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.32
X-RAY DIFFRACTIONc_mcbond_it1.2481.5
X-RAY DIFFRACTIONc_scbond_it1.8292
X-RAY DIFFRACTIONc_mcangle_it2.0842
X-RAY DIFFRACTIONc_scangle_it2.782.5
LS refinement shellResolution: 2.45→2.48 Å / Total num. of bins used: 32
RfactorNum. reflection% reflection
Rfree0.3676 30 3.783 %
Rwork0.3058 763 -
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 20 Å / Num. reflection obs: 32148 / Num. reflection Rfree: 1559 / Rfactor Rfree: 0.261 / Rfactor Rwork: 0.201 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

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