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- PDB-1yaf: Structure of TenA from Bacillus subtilis -

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Basic information

Entry
Database: PDB / ID: 1yaf
TitleStructure of TenA from Bacillus subtilis
ComponentsTranscriptional activator tenA
KeywordsTRANSCRIPTION / Thiaminase
Function / homology
Function and homology information


aminopyrimidine aminohydrolase / thiaminase activity / thiamine biosynthetic process / thiamine diphosphate biosynthetic process / cytosol
Similarity search - Function
Thiaminase II / : / Thiaminase-2/PQQC / TENA/THI-4/PQQC family / Heme oxygenase-like / Heme Oxygenase; Chain A / Haem oxygenase-like, multi-helical / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Aminopyrimidine aminohydrolase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsToms, A.V. / Haas, A.L. / Park, J.-H. / Begley, T.P. / Ealick, S.E.
CitationJournal: Biochemistry / Year: 2005
Title: Structural characterization of the regulatory proteins TenA and TenI from Bacillus subtilis and identification of TenA as a thiaminase II.
Authors: Toms, A.V. / Haas, A.L. / Park, J.H. / Begley, T.P. / Ealick, S.E.
History
DepositionDec 17, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcriptional activator tenA
B: Transcriptional activator tenA
C: Transcriptional activator tenA
D: Transcriptional activator tenA


Theoretical massNumber of molelcules
Total (without water)122,2804
Polymers122,2804
Non-polymers00
Water2,648147
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8100 Å2
ΔGint-50 kcal/mol
Surface area35220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.428, 58.259, 297.017
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Detailsthe biological unit is a tetramer. The asymmetric unit contains 1 biological unit.

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Components

#1: Protein
Transcriptional activator tenA


Mass: 30569.998 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: tenA / Plasmid: pDESTF1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P25052
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / 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: 2.3 Å3/Da / Density % sol: 45 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 4.4
Details: 26% MPD 20 mM CaCl2, pH 4.4, VAPOR DIFFUSION, HANGING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 8-BM / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 24, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.6→40 Å / Num. all: 30807 / Num. obs: 30415 / % possible obs: 94.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2.8 % / Biso Wilson estimate: 26.2 Å2 / Rsym value: 0.088 / Net I/σ(I): 13.3
Reflection shellResolution: 2.6→2.76 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 6.85 / Num. unique all: 4634 / Rsym value: 0.216 / % possible all: 87.4

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Processing

Software
NameVersionClassification
CNS1.1refinement
ADSCdata collection
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: homology model built from PDB entries 1UDD and 1RTW

1udd

1rtw


Resolution: 2.6→39.75 Å / Rfactor Rfree error: 0.001 / Data cutoff high absF: 270453.44 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.284 28907 95 %RANDOM
Rwork0.231 ---
all0.237 30807 --
obs0.231 30415 94.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 39.662 Å2 / ksol: 0.345707 e/Å3
Displacement parametersBiso mean: 48.7 Å2
Baniso -1Baniso -2Baniso -3
1-3.61 Å20 Å20 Å2
2--10.82 Å20 Å2
3----14.43 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.42 Å
Luzzati d res low-5 Å
Luzzati sigma a0.26 Å0.36 Å
Refinement stepCycle: LAST / Resolution: 2.6→39.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7240 0 0 147 7387
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d17.9
X-RAY DIFFRACTIONc_improper_angle_d0.67
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.004 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.341 4414 95.3 %
Rwork0.271 220 -
obs--87.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP

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