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- PDB-1yad: Structure of TenI from Bacillus subtilis -

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Basic information

Entry
Database: PDB / ID: 1yad
TitleStructure of TenI from Bacillus subtilis
ComponentsRegulatory protein tenI
KeywordsTRANSCRIPTION / TIM barrel
Function / homology
Function and homology information


thiazole tautomerase / thiamine-phosphate diphosphorylase activity / thiamine diphosphate biosynthetic process / thiamine biosynthetic process / isomerase activity / cytoplasm
Similarity search - Function
Thiamine phosphate synthase/TenI / Thiamine monophosphate synthase / Thiamin phosphate synthase superfamily / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
TRIS-HYDROXYMETHYL-METHYL-AMMONIUM / Thiazole tautomerase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 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 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: Regulatory protein tenI
B: Regulatory protein tenI
C: Regulatory protein tenI
D: Regulatory protein tenI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,23715
Polymers99,1024
Non-polymers1,13511
Water9,782543
1
A: Regulatory protein tenI
B: Regulatory protein tenI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,1808
Polymers49,5512
Non-polymers6296
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3280 Å2
ΔGint-86 kcal/mol
Surface area16310 Å2
MethodPISA
2
C: Regulatory protein tenI
D: Regulatory protein tenI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,0577
Polymers49,5512
Non-polymers5065
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2930 Å2
ΔGint-87 kcal/mol
Surface area15920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.836, 103.778, 217.051
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsThe biological assembly is a dimer. The asymmetric unit contains 2 biological units.

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Components

#1: Protein
Regulatory protein tenI


Mass: 24775.539 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: tenI / Plasmid: pET-28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P25053
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-144 / TRIS-HYDROXYMETHYL-METHYL-AMMONIUM


Mass: 122.143 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H12NO3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 543 / 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: 2.99 Å3/Da / Density % sol: 57 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 9
Details: ammonium sulfate, pH 9.0, 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: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 24, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 72558 / Num. obs: 61326 / % possible obs: 95.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.8 % / Biso Wilson estimate: 14.2 Å2 / Rsym value: 0.088 / Net I/σ(I): 18.8
Reflection shellResolution: 2.1→2.23 Å / Redundancy: 5.8 % / Mean I/σ(I) obs: 4.3 / Num. unique all: 9652 / Rsym value: 0.396 / % possible all: 91.5

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Processing

Software
NameVersionClassification
CNS1.1refinement
ADSCdata collection
HKL-2000data scaling
SnBCNS1.1phasing
RefinementMethod to determine structure: SAD / Resolution: 2.1→37.01 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 138911.41 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.221 3117 5.1 %RANDOM
Rwork0.196 ---
all0.2 72558 --
obs0.196 61326 95.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 51.9234 Å2 / ksol: 0.373938 e/Å3
Displacement parametersBiso mean: 26.8 Å2
Baniso -1Baniso -2Baniso -3
1-4.47 Å20 Å20 Å2
2--1.41 Å20 Å2
3----5.88 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 2.1→37.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5898 0 64 543 6505
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.4
X-RAY DIFFRACTIONc_improper_angle_d0.76
X-RAY DIFFRACTIONc_mcbond_it1.511.5
X-RAY DIFFRACTIONc_mcangle_it2.212
X-RAY DIFFRACTIONc_scbond_it2.532
X-RAY DIFFRACTIONc_scangle_it3.632.5
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.252 495 5.1 %
Rwork0.213 9157 -
obs--91.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4TRIS.PARAMTRIS.TOP

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