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

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Basic information

Entry
Database: PDB / ID: 1bko
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 / cytoplasm / cytosol
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 / MIR/molecular replacement / Resolution: 2.75 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 9, 1998Processing site: BNL
Revision 1.0Feb 2, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 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
C: THYMIDYLATE SYNTHASE A
D: THYMIDYLATE SYNTHASE A


Theoretical massNumber of molelcules
Total (without water)130,8684
Polymers130,8684
Non-polymers00
Water63135
1
A: THYMIDYLATE SYNTHASE A
B: THYMIDYLATE SYNTHASE A


Theoretical massNumber of molelcules
Total (without water)65,4342
Polymers65,4342
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4570 Å2
ΔGint-6 kcal/mol
Surface area23420 Å2
MethodPISA
2
C: THYMIDYLATE SYNTHASE A
D: THYMIDYLATE SYNTHASE A


Theoretical massNumber of molelcules
Total (without water)65,4342
Polymers65,4342
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4410 Å2
ΔGint-5 kcal/mol
Surface area23690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.363, 52.828, 129.391
Angle α, β, γ (deg.)90.00, 101.70, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.999732, -0.022933, -0.003207), (-0.021468, 0.969811, -0.242913), (0.008681, -0.242779, -0.970043)40.6928, 8.4761, 64.9447
2given(-0.920918, 0.038337, 0.387866), (-0.031905, -0.999226, 0.023011), (0.388448, 0.008817, 0.921429)9.09847, 45.70549, 57.77644
3given(0.925561, -0.045288, -0.375881), (0.051774, -0.968352, 0.24416), (-0.375043, -0.245446, -0.893924)-3.19579, 36.84923, 133.2341

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Components

#1: Protein
THYMIDYLATE SYNTHASE A


Mass: 32716.980 Da / Num. of mol.: 4
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
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / 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: 2.75 Å3/Da / Density % sol: 51.3 %
Crystal growpH: 6.5 / Details: pH 6.5
Crystal grow
*PLUS
Temperature: 22 ℃ / pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
220 mM1reservoirKPO4

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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: Apr 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: 2.75→50 Å / Num. obs: 31528 / % possible obs: 90.9 % / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Biso Wilson estimate: 22.7 Å2 / Rmerge(I) obs: 0.091 / Rsym value: 0.086 / Net I/σ(I): 8.4
Reflection shellResolution: 2.75→2.83 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.366 / Mean I/σ(I) obs: 3.9 / Rsym value: 0.315 / % possible all: 81.8
Reflection
*PLUS
Num. measured all: 80025
Reflection shell
*PLUS
% possible obs: 81.8 %

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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: MIR/molecular replacement
Starting model: HOMOLOGY MODEL BASED ON 1TJS

1tjs


Resolution: 2.75→50 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.32 2743 10.4 %SHELLS
Rwork0.213 ---
obs0.213 26480 76.1 %-
Displacement parametersBiso mean: 17.9 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.33 Å
Luzzati d res low-8 Å
Luzzati sigma a0.65 Å0.45 Å
Refinement stepCycle: LAST / Resolution: 2.75→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9204 0 0 35 9239
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_deg1.3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.4
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.17
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it3.241.5
X-RAY DIFFRACTIONx_mcangle_it4.882
X-RAY DIFFRACTIONx_scbond_it4.822
X-RAY DIFFRACTIONx_scangle_it6.632.5
LS refinement shellResolution: 2.75→2.92 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.375 197 6.5 %
Rwork0.271 2833 -
obs--52.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
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_deg24.4
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.17
LS refinement shell
*PLUS
Rfactor obs: 0.271

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