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- PDB-1tyg: Structure of the thiazole synthase/ThiS complex -

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Basic information

Entry
Database: PDB / ID: 1tyg
TitleStructure of the thiazole synthase/ThiS complex
Components
  • Thiazole biosynthesis protein thiG
  • yjbS
KeywordsBIOSYNTHETIC PROTEIN / alpha beta barrel / protein-protein complex / ThiS / ThiG
Function / homology
Function and homology information


thiazole synthase activity / thiazole synthase / thiamine diphosphate biosynthetic process / thiamine biosynthetic process / nucleotide binding / cytoplasm
Similarity search - Function
Thiazole synthase / ThiS, thiamine-biosynthesis / Thiazole synthase ThiG / Thiazole biosynthesis protein ThiG / Sulfur carrier ThiS/MoaD-like / ThiS family / Molybdopterin synthase/thiamin biosynthesis sulphur carrier, beta-grasp / Beta-grasp domain / Beta-grasp domain superfamily / Ubiquitin-like (UB roll) ...Thiazole synthase / ThiS, thiamine-biosynthesis / Thiazole synthase ThiG / Thiazole biosynthesis protein ThiG / Sulfur carrier ThiS/MoaD-like / ThiS family / Molybdopterin synthase/thiamin biosynthesis sulphur carrier, beta-grasp / Beta-grasp domain / Beta-grasp domain superfamily / Ubiquitin-like (UB roll) / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Roll / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Sulfur carrier protein ThiS / Thiazole synthase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.15 Å
AuthorsSettembre, E.C. / Dorrestein, P.C. / Zhai, H. / Chatterjee, A. / McLafferty, F.W. / Begley, T.P. / Ealick, S.E.
CitationJournal: Biochemistry / Year: 2004
Title: Thiamin Biosynthesis in Bacillus subtilis: Structure of the Thiazole Synthase/Sulfur Carrier Protein Complex
Authors: Settembre, E.C. / Dorrestein, P.C. / Zhai, H. / Chatterjee, A. / McLafferty, F.W. / Begley, T.P. / Ealick, S.E.
History
DepositionJul 7, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Feb 14, 2024Group: 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 / struct_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _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
B: yjbS
A: Thiazole biosynthesis protein thiG
C: Thiazole biosynthesis protein thiG
G: yjbS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,8466
Polymers73,6564
Non-polymers1902
Water905
1
B: yjbS
A: Thiazole biosynthesis protein thiG
C: Thiazole biosynthesis protein thiG
G: yjbS
hetero molecules

B: yjbS
A: Thiazole biosynthesis protein thiG
C: Thiazole biosynthesis protein thiG
G: yjbS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,69312
Polymers147,3138
Non-polymers3804
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Unit cell
Length a, b, c (Å)91.654, 91.654, 401.300
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
31A
41C
51A
61C
71A
81C
91A
101C

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEUALAALA2AB104 - 1432 - 41
21LEULEUALAALA2CC104 - 1432 - 41
32LEULEUSERSER6AB161 - 16459 - 62
42LEULEUSERSER6CC161 - 16459 - 62
53ILEILELEULEU6AB339 - 341237 - 239
63ILEILELEULEU6CC339 - 341237 - 239
74LYSLYSARGARG4AB165 - 33863 - 236
84LYSLYSARGARG4CC165 - 33863 - 236
95ILEILEGLNGLN6AB149 - 16047 - 58
105PHEPHEGLNGLN6CC150 - 16048 - 58

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Components

#1: Protein yjbS


Mass: 10099.463 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Plasmid: pET-16b / Production host: Escherichia coli (E. coli) / References: UniProt: O31617
#2: Protein Thiazole biosynthesis protein thiG


Mass: 26728.758 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: thiG,BSU11690 / Plasmid: pET-16b / Production host: Escherichia coli (E. coli) / References: UniProt: O31618
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / 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: 3.3 Å3/Da / Density % sol: 62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.15
Details: 5% PEG 8K, 200 mM Sodium Chloride, 100 mM sodium phosphate pH 6.1, pH 7.15, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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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 10, 2003
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 3.15→15 Å / Num. all: 17866 / Num. obs: 17866 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 %
Reflection shellResolution: 3.15→3.26 Å / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 3.15→15 Å / Cor.coef. Fo:Fc: 0.89 / Cor.coef. Fo:Fc free: 0.814 / SU B: 23.889 / SU ML: 0.428 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R Free: 0.534 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.3046 1261 7.3 %RANDOM
Rwork0.24231 ---
all0.24231 17866 --
obs0.24691 15975 95.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 45.572 Å2
Baniso -1Baniso -2Baniso -3
1-2.14 Å21.07 Å20 Å2
2--2.14 Å20 Å2
3----3.21 Å2
Refinement stepCycle: LAST / Resolution: 3.15→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4540 0 10 5 4555
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0224610
X-RAY DIFFRACTIONr_angle_refined_deg2.0221.9916247
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.5555603
X-RAY DIFFRACTIONr_chiral_restr0.1310.2746
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023381
X-RAY DIFFRACTIONr_nbd_refined0.2680.22364
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1850.2141
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2340.244
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2940.26
X-RAY DIFFRACTIONr_mcbond_it0.4931.53012
X-RAY DIFFRACTIONr_mcangle_it0.92724816
X-RAY DIFFRACTIONr_scbond_it1.60731598
X-RAY DIFFRACTIONr_scangle_it2.7414.51431
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
152tight positional0.070.05
1379medium positional0.430.5
114loose positional0.745
152tight thermal0.20.5
1379medium thermal0.912
114loose thermal2.0810
LS refinement shellResolution: 3.15→3.228 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.375 66
Rwork0.271 1018
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
110.79066.8954-3.20089.3717-6.83067.73730.5527-0.97810.87661.4122-0.15440.98390.1757-0.7212-0.39831.0929-0.46870.06220.29490.02620.4097-47.7597-7.26835.7806
22.33970.64430.4221.92132.05946.48340.4465-0.1363-0.11560.23980.3331-0.17270.18680.752-0.77950.4574-0.1029-0.03010.067-0.10710.2978-25.52054.492416.9759
34.4528-0.5941-0.33111.09380.56653.76120.4190.13340.4778-0.16960.6486-1.1545-0.52232.6883-1.06770.451-0.34330.20562.2127-0.95511.21669.760111.798712.2642
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1BA1 - 6522 - 86
2X-RAY DIFFRACTION2AB103 - 3441 - 242
3X-RAY DIFFRACTION2AE1400
4X-RAY DIFFRACTION3CC104 - 1432 - 41
5X-RAY DIFFRACTION3CF2400
6X-RAY DIFFRACTION3CC150 - 34548 - 243

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