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- PDB-1bsf: THERMOSTABLE THYMIDYLATE SYNTHASE A FROM BACILLUS SUBTILIS -

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Basic information

Entry
Database: PDB / ID: 1bsf
TitleTHERMOSTABLE THYMIDYLATE SYNTHASE A FROM BACILLUS SUBTILIS
ComponentsTHYMIDYLATE SYNTHASE A
KeywordsMETHYLTRANSFERASE / DTMP SYNTHASE
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, active site / Thymidylate synthase active site. / Thymidylate synthase / Thymidylate synthase/dCMP hydroxymethylase / Thymidylate synthase/dCMP hydroxymethylase domain / Thymidylate synthase/dCMP hydroxymethylase superfamily / Thymidylate synthase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Thymidylate synthase 1 / Thymidylate synthase 1
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsStout, T.J. / Schellenberger, U. / Santi, D.V. / Stroud, R.M.
Citation
Journal: Biochemistry / Year: 1998
Title: Crystal structures of a unique thermal-stable thymidylate synthase from Bacillus subtilis.
Authors: Stout, T.J. / Schellenberger, U. / Santi, D.V. / Stroud, R.M.
#1: Journal: Protein Sci. / Year: 1994
Title: Expression, Purification, and Characterization of Thymidylate Synthase from Lactococcus Lactis
Authors: Greene, P.J. / Yu, P.L. / Zhao, J. / Schiffer, C.A. / Santi, D.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1978
Title: Two Thymidylate Synthetases in Bacillus Subtilis
Authors: Neuhard, J. / Price, A.R. / Schack, L. / Thomassen, E.
History
DepositionJul 10, 1998Processing site: BNL
Revision 1.0Jan 13, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Refinement description / Category: database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: THYMIDYLATE SYNTHASE A
B: THYMIDYLATE SYNTHASE A


Theoretical massNumber of molelcules
Total (without water)65,4342
Polymers65,4342
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4390 Å2
ΔGint-4 kcal/mol
Surface area23020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.982, 95.962, 143.880
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: given
Matrix: (0.363337, 0.262697, 0.893855), (0.257455, -0.950375, 0.174657), (0.895379, 0.166668, -0.412939)
Vector: -13.638, 26.7253, 13.2341)

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Components

#1: Protein THYMIDYLATE SYNTHASE A


Mass: 32716.980 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Cell line: X2913 / Gene: THYA / Plasmid: PTRC-THYA / Cell line (production host): X2913 / Gene (production host): THYA / Production host: Escherichia coli (E. coli)
References: UniProt: P42326, UniProt: P0CI79*PLUS, thymidylate synthase

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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: 3.12 Å3/Da / Density % sol: 60.3 %
Crystal growpH: 6.5 / Details: pH 6.5
Crystal grow
*PLUS
Temperature: 22 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
220 mMTris-HCl1drop
30.1 mMEDTA1drop
41 mMdithiothreitol1drop

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Jun 1, 1996 / Details: COLLIMATOR
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 82603 / % possible obs: 23.1 % / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Biso Wilson estimate: 5.9 Å2 / Rsym value: 0.084 / Net I/σ(I): 6.9
Reflection shellResolution: 2.2→2.26 Å / Redundancy: 1.6 % / Mean I/σ(I) obs: 1.6 / Rsym value: 0.287 / % possible all: 19.4
Reflection
*PLUS
Num. obs: 31281 / Num. measured all: 82603 / Rmerge(I) obs: 0.084
Reflection shell
*PLUS
% possible obs: 19.4 % / Rmerge(I) obs: 0.287

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Processing

Software
NameVersionClassification
AMoREphasing
DMmodel building
MLPHAREphasing
X-PLORmodel building
X-PLOR3.854refinement
DENZOdata reduction
SCALEPACKdata scaling
DMphasing
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: HOMOLOGY MODEL BASED ON 1TJS

1tjs


Resolution: 2.2→60 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.301 911 10.3 %SHELLS
Rwork0.195 ---
obs0.195 32200 23.1 %-
Displacement parametersBiso mean: 22.8 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.48 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.62 Å0.34 Å
Refinement stepCycle: LAST / Resolution: 2.2→60 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2301 0 0 0 2301
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.007
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_deg1.2
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.6
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.6
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.931.5
X-RAY DIFFRACTIONx_mcangle_it4.272
X-RAY DIFFRACTIONx_scbond_it4.372
X-RAY DIFFRACTIONx_scangle_it5.572.5
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.038 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.362 102 9.8 %
Rwork0.287 934 -
obs--19.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PRTOPHCSDX.PR
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
Software
*PLUS
Name: X-PLOR / Version: 3.854 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.6
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.6
LS refinement shell
*PLUS
Rfactor obs: 0.287

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