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

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Basic information

Entry
Database: PDB / ID: 1bkp
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 / MIR/molecular replacement / Resolution: 1.7 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 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Other / Refinement description
Category: database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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
Water6,287349
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4410 Å2
ΔGint-8 kcal/mol
Surface area22950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.940, 81.630, 64.790
Angle α, β, γ (deg.)90.00, 92.52, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.127578, 0.019096, -0.991645), (0.0181, -0.999693, -0.016922), (-0.991663, -0.01579, -0.127885)
Vector: 28.5314, 0.2384, 32.5053)

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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
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 349 / 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: 2.42 Å3/Da / Density % sol: 48.8 %
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: Jul 1, 1995 / Details: COLLIMATOR
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 60767 / % possible obs: 88.9 % / Observed criterion σ(I): -3 / Redundancy: 5.4 % / Biso Wilson estimate: 10.8 Å2 / Rmerge(I) obs: 0.086 / Rsym value: 0.086 / Net I/σ(I): 13.2
Reflection shellResolution: 1.7→1.75 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.315 / Mean I/σ(I) obs: 3.1 / Rsym value: 0.315 / % possible all: 56.5
Reflection
*PLUS
Num. measured all: 208765
Reflection shell
*PLUS
% possible obs: 56.5 %

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Processing

Software
NameVersionClassification
X-PLOR3.843model building
X-PLOR3.843refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.843phasing
RefinementMethod to determine structure: MIR/molecular replacement
Starting model: HOMOLOGY MODEL BASED ON 1TJS

1tjs


Resolution: 1.7→48.3 Å / Rfactor Rfree error: 0.005 / 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
Rfree0.206 2505 4.1 %SHELLS
Rwork0.151 ---
obs0.151 60736 88.9 %-
Displacement parametersBiso mean: 24.9 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.19 Å0.16 Å
Luzzati d res low-5 Å
Luzzati sigma a0.12 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 1.7→48.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4602 0 0 350 4952
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_deg1.3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.2
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.11
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.511.5
X-RAY DIFFRACTIONx_mcangle_it3.862
X-RAY DIFFRACTIONx_scbond_it8.362
X-RAY DIFFRACTIONx_scangle_it13.32.5
LS refinement shellResolution: 1.7→1.81 Å / Rfactor Rfree error: 0.087 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.213 225 4 %
Rwork0.178 5399 -
obs--48.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
Software
*PLUS
Name: X-PLOR / Version: 3.843 / 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_deg24.2
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.11
LS refinement shell
*PLUS
Rfactor obs: 0.178

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