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- PDB-1b02: CRYSTAL STRUCTURE OF THYMIDYLATE SYNTHASE A FROM BACILLUS SUBTILIS -

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Basic information

Entry
Database: PDB / ID: 1b02
TitleCRYSTAL STRUCTURE OF THYMIDYLATE SYNTHASE A FROM BACILLUS SUBTILIS
ComponentsPROTEIN (THYMIDYLATE SYNTHASE)
KeywordsTRANSFERASE / METHYLTRANSFERASE
Function / homology
Function and homology information


thymidylate synthase / thymidylate synthase activity / dTMP biosynthetic process / dTTP biosynthetic process / methylation / cytosol / cytoplasm
Similarity search - Function
Thymidylate Synthase; Chain A / Thymidylate synthase/dCMP hydroxymethylase domain / Thymidylate synthase/dCMP hydroxymethylase / Thymidylate synthase, active site / Thymidylate synthase active site. / Thymidylate synthase / Thymidylate synthase/dCMP hydroxymethylase domain / Thymidylate synthase/dCMP hydroxymethylase superfamily / Thymidylate synthase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
5-METHYL-5,6,7,8-TETRAHYDROFOLIC ACID / 5-FLUORO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE / Thymidylate synthase 1 / Thymidylate synthase 1
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsFox, K.M. / Maley, F. / Garibian, A. / Changchien, L. / Vanroey, P.
CitationJournal: Protein Sci. / Year: 1999
Title: Crystal structure of thymidylate synthase A from Bacillus subtilis.
Authors: Fox, K.M. / Maley, F. / Garibian, A. / Changchien, L.M. / Van Roey, P.
History
DepositionNov 16, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Mar 29, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jan 29, 2014Group: Other
Revision 1.4Aug 9, 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_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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: PROTEIN (THYMIDYLATE SYNTHASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6343
Polymers32,8481
Non-polymers7862
Water1,51384
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.570, 105.010, 117.260
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: generate
Matrix: (-0.9401, 0.3213, -0.114), (0.3228, 0.7314, -0.6008), (-0.1097, -0.6016, -0.7913)
Vector: -7.3565, 24.608, 66.7055)

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Components

#1: Protein PROTEIN (THYMIDYLATE SYNTHASE)


Mass: 32848.176 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Plasmid: PET17XB / Production host: Escherichia coli (E. coli) / Strain (production host): DH5ALPHA
References: UniProt: P42326, UniProt: P0CI79*PLUS, thymidylate synthase
#2: Chemical ChemComp-UFP / 5-FLUORO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE / Fluorodeoxyuridylate


Type: DNA linking / Mass: 326.172 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H12FN2O8P / Comment: inhibitor*YM
#3: Chemical ChemComp-C2F / 5-METHYL-5,6,7,8-TETRAHYDROFOLIC ACID / Levomefolic acid


Mass: 459.456 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H25N7O6
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 84 / 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: 2.8 Å3/Da / Density % sol: 50 %
Crystal growpH: 6.25 / Details: pH 6.25
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
18.4 mg/mlB subtlis thymidine synthase1drop
21 mM(R,S)-CH2H4-folate1drop
33 mMFdUMP1drop
420 mMphosphate1drop
51 mMdithiothreitol1drop
623 %PEG40001reservoir
70.1 Msodium citrate1reservoir
80.2 Mammonium acetate1reservoir
910 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jul 1, 1998 / Details: MSC MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 23792 / % possible obs: 96 % / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Rsym value: 0.094
Reflection shellResolution: 2.47→2.51 Å / Rsym value: 0.349 / % possible all: 79.3
Reflection
*PLUS
Rmerge(I) obs: 0.094
Reflection shell
*PLUS
% possible obs: 79.3 % / Rmerge(I) obs: 0.349

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1TSN

1tsn


Resolution: 2.5→100 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.233 2280 9.6 %RANDOM
Rwork0.194 ---
obs-23755 97.2 %-
Displacement parametersBiso mean: 29.7 Å2
Refinement stepCycle: LAST / Resolution: 2.5→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2315 0 54 84 2453
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.1
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.5
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.48
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it41.5
X-RAY DIFFRACTIONx_mcangle_it5.62
X-RAY DIFFRACTIONx_scbond_it6.42
X-RAY DIFFRACTIONx_scangle_it8.62.5
Refine LS restraints NCSNCS model details: CONSTRAINTS
LS refinement shellResolution: 2.5→2.61 Å / Total num. of bins used: 8
Rfactor% reflection
Rfree0.366 9.8 %
Rwork0.297 -
obs-87.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.194
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.5
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.48
LS refinement shell
*PLUS
Rfactor obs: 0.297

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