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- PDB-3qh2: Crystal structure of TenI from Bacillus subtilis complexed with p... -

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Basic information

Entry
Database: PDB / ID: 3qh2
TitleCrystal structure of TenI from Bacillus subtilis complexed with product cThz-P
ComponentsRegulatory protein tenI
KeywordsISOMERASE / Alpha-Beta 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
Chem-3NM / Thiazole tautomerase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.231 Å
AuthorsHan, Y. / Zhang, Y. / Hazra, A. / Chatterjee, A. / Lai, R. / Begley, T.P. / Ealick, S.E.
CitationJournal: J.Am.Chem.Soc. / Year: 2011
Title: A Missing Enzyme in Thiamin Thiazole Biosynthesis: Identification of TenI as a Thiazole Tautomerase.
Authors: Hazra, A.B. / Han, Y. / Chatterjee, A. / Zhang, Y. / Lai, R.Y. / Ealick, S.E. / Begley, T.P.
History
DepositionJan 25, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / 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

Downloads & links

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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)100,2679
Polymers99,1024
Non-polymers1,1655
Water5,441302
1
A: Regulatory protein tenI
B: Regulatory protein tenI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,1825
Polymers49,5512
Non-polymers6303
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1920 Å2
ΔGint-32 kcal/mol
Surface area16980 Å2
MethodPISA
2
C: Regulatory protein tenI
D: Regulatory protein tenI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,0854
Polymers49,5512
Non-polymers5342
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1550 Å2
ΔGint-11 kcal/mol
Surface area16780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.047, 105.418, 219.260
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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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, BSU11660 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P25053
#2: Chemical
ChemComp-3NM / 4-methyl-5-[2-(phosphonooxy)ethyl]-1,3-thiazole-2-carboxylic acid


Mass: 267.196 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C7H10NO6PS
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 302 / 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: 2.86 Å3/Da / Density % sol: 56.97 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.7
Details: ammonium sulfate, PEG 400, bicine, cysteine, pH 8.7, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.9777 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 2, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9777 Å / Relative weight: 1
ReflectionResolution: 2.23→50 Å / Num. all: 55489 / Num. obs: 55489 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 6.1 % / Rmerge(I) obs: 0.096 / Χ2: 1.107 / Net I/σ(I): 9.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.23-2.316.40.45154781.3911100
2.31-2.46.40.38155421.2991100
2.4-2.516.30.30854641.146199.9
2.51-2.646.20.23955081.151199.9
2.64-2.816.10.18154880.998199.9
2.81-3.035.90.12855090.979199.7
3.03-3.335.80.08455330.966199.6
3.33-3.815.70.05555661.022199.5
3.81-4.85.80.03856130.954199.8
4.8-506.30.03557881.114199.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.6.4_486refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1YAD

1yad


Resolution: 2.231→42.751 Å / Occupancy max: 1 / Occupancy min: 0.41 / FOM work R set: 0.8543 / SU ML: 0.29 / σ(F): 1.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2228 2801 5.08 %RANDOM
Rwork0.1735 ---
obs0.176 55149 99.19 %-
all-55489 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.977 Å2 / ksol: 0.402 e/Å3
Displacement parametersBiso max: 85.73 Å2 / Biso mean: 24.6369 Å2 / Biso min: 0.38 Å2
Baniso -1Baniso -2Baniso -3
1-2.9164 Å2-0 Å2-0 Å2
2---0.1022 Å2-0 Å2
3----2.8141 Å2
Refinement stepCycle: LAST / Resolution: 2.231→42.751 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6024 0 69 302 6395
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0116238
X-RAY DIFFRACTIONf_angle_d1.2658418
X-RAY DIFFRACTIONf_chiral_restr0.074963
X-RAY DIFFRACTIONf_plane_restr0.0041088
X-RAY DIFFRACTIONf_dihedral_angle_d14.3942340
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2307-2.26920.30231560.20722514267098
2.2692-2.31040.24171330.17812597273099
2.3104-2.35490.26761370.18412576271399
2.3549-2.40290.29071400.19182649278999
2.4029-2.45520.25831240.18972567269199
2.4552-2.51230.27211530.184825922745100
2.5123-2.57510.24071380.193825992737100
2.5751-2.64470.24551350.196326272762100
2.6447-2.72250.26931350.184825952730100
2.7225-2.81040.21921520.190425942746100
2.8104-2.91080.25371280.186526352763100
2.9108-3.02730.22351440.183326082752100
3.0273-3.16510.22681400.17712627276799
3.1651-3.33190.20781350.171726242759100
3.3319-3.54050.20441350.1542651278699
3.5405-3.81370.21941360.162226402776100
3.8137-4.19720.18631410.145426462787100
4.1972-4.80390.16581650.132526582823100
4.8039-6.04970.20271480.165626812829100
6.0497-42.7590.22491260.20962668279495

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