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- PDB-5z9y: Crystal structure of Mycobacterium tuberculosis thiazole synthase... -

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Basic information

Entry
Database: PDB / ID: 5z9y
TitleCrystal structure of Mycobacterium tuberculosis thiazole synthase (ThiG) complexed with DXP
ComponentsThiazole synthase
KeywordsTRANSFERASE / alpha-beta barrel / covalently bound / carbinolamine intermediate / BIOSYNTHETIC PROTEIN
Function / homology
Function and homology information


thiazole synthase / sulfurtransferase activity / thiamine diphosphate biosynthetic process / thiamine biosynthetic process / cytoplasm
Similarity search - Function
Thiazole synthase / Thiazole synthase ThiG / Thiazole biosynthesis protein ThiG / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
1-DEOXY-D-XYLULOSE-5-PHOSPHATE / Thiazole synthase
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.48 Å
AuthorsZhang, J. / Zhang, B. / Zhao, Y. / Yang, X. / Huang, M. / Cui, P. / Zhang, W. / Li, J. / Zhang, Y.
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2018
Title: Snapshots of catalysis: Structure of covalently bound substrate trapped in Mycobacterium tuberculosis thiazole synthase (ThiG).
Authors: Zhang, J. / Zhang, B. / Zhao, Y. / Yang, X. / Huang, M. / Cui, P. / Zhang, W. / Li, J. / Zhang, Y.
History
DepositionFeb 5, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 11, 2018Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Thiazole synthase
B: Thiazole synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,1624
Polymers51,7332
Non-polymers4282
Water6,323351
1
A: Thiazole synthase
hetero molecules

A: Thiazole synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,1624
Polymers51,7332
Non-polymers4282
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_545x,x-y-1,-z+1/61
Buried area4380 Å2
ΔGint-29 kcal/mol
Surface area17950 Å2
MethodPISA
2
B: Thiazole synthase
hetero molecules

B: Thiazole synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,1624
Polymers51,7332
Non-polymers4282
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_545x,x-y-1,-z+1/61
Buried area4680 Å2
ΔGint-28 kcal/mol
Surface area18010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.670, 116.670, 123.320
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Thiazole synthase


Mass: 25866.656 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: thiG, Rv0417, MTCY22G10.14 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P9WG73, thiazole synthase
#2: Chemical ChemComp-DXP / 1-DEOXY-D-XYLULOSE-5-PHOSPHATE


Mass: 214.110 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C5H11O7P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 351 / 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: 2.34 Å3/Da / Density % sol: 47.47 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 0.2 M sodium malonate pH 5.0, 20% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97852 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 14, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97852 Å / Relative weight: 1
ReflectionResolution: 1.48→61.66 Å / Num. obs: 82214 / % possible obs: 99.7 % / Redundancy: 36.1 % / Rpim(I) all: 0.014 / Rrim(I) all: 0.088 / Net I/σ(I): 26.2 / Num. measured all: 2970865
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) all% possible all
1.48-1.5120.41.47913738810.5212.40895.6
4.02-61.7133.990.615247745000.0070.041100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
xia2data scaling
PDB_EXTRACT3.24data extraction
PHASERphasing
XDSdata reduction
RefinementResolution: 1.48→58.335 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 17.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1884 4063 4.95 %
Rwork0.1634 78088 -
obs0.1646 82151 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 72.54 Å2 / Biso mean: 26.6034 Å2 / Biso min: 14.74 Å2
Refinement stepCycle: final / Resolution: 1.48→58.335 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3352 0 26 351 3729
Biso mean--33.97 38.37 -
Num. residues----466
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0213428
X-RAY DIFFRACTIONf_angle_d1.8554690
X-RAY DIFFRACTIONf_chiral_restr0.118592
X-RAY DIFFRACTIONf_plane_restr0.01603
X-RAY DIFFRACTIONf_dihedral_angle_d12.211220
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 29

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.48-1.49740.31041130.27492577269096
1.4974-1.51570.25381240.25862589271397
1.5157-1.53490.25461470.24042575272298
1.5349-1.55510.26981470.22652642278999
1.5551-1.57640.23071390.20822642278199
1.5764-1.59890.22351560.199726622818100
1.5989-1.62280.21491530.197926462799100
1.6228-1.64810.21851650.185526302795100
1.6481-1.67520.21671490.178226382787100
1.6752-1.7040.19121320.170526992831100
1.704-1.7350.19411240.169926852809100
1.735-1.76840.16741370.164927012838100
1.7684-1.80450.20271550.157726372792100
1.8045-1.84370.20671420.15426762818100
1.8437-1.88660.17631320.155326862818100
1.8866-1.93380.1831460.151926662812100
1.9338-1.98610.17631480.145726822830100
1.9861-2.04450.19181300.14927192849100
2.0445-2.11050.20151590.152126572816100
2.1105-2.1860.18571310.147727052836100
2.186-2.27350.17521620.151226852847100
2.2735-2.3770.19281380.153227292867100
2.377-2.50230.161270.15827062833100
2.5023-2.65910.20611380.159627462884100
2.6591-2.86440.17251420.165727212863100
2.8644-3.15260.18041180.164527922910100
3.1526-3.60870.18281330.159127752908100
3.6087-4.54640.16871260.151528352961100
4.5464-58.38030.19541500.173629853135100
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)
10.3174-0.0926-0.02920.1170.22030.27490.03670.08770.01560.0031-0.05290.1039-0.0132-0.16630.00010.2114-0.00060.01770.2793-0.01560.211642.2377-22.32446.896
20.16580.06340.00110.2547-0.01660.2925-0.27550.25150.1567-0.66630.06220.1879-0.0082-0.1923-0.03170.23510.0311-0.02750.25790.03690.314441.6423-5.85378.9002
30.31750.00510.19540.56490.03460.4977-0.0566-0.03310.15580.01730.01360.0072-0.1380.027200.2243-0.00890.02490.2179-0.01650.26351.7191-6.569515.9201
40.27560.0437-0.16260.48340.16480.3576-0.0061-0.00390.0137-0.0043-0.00710.0003-0.00820.00960.00010.1939-0.00180.00120.2048-0.01150.179259.901-24.942713.3166
50.0713-0.07310.07780.38940.12940.1796-0.0203-0.02190.15180.16550.091-0.1952-0.14790.00470.00030.26420.0037-0.01410.1951-0.01350.235392.0230.794322.8351
60.5795-0.3340.080.77480.09270.4964-0.0141-0.01290.0354-0.00850.03250.0457-0.0323-0.0118-00.1818-0.00670.01250.1690.00710.191577.6033-1.327418.2316
70.0030.0129-0.00260.0363-0.00350.0048-0.04860.13130.0589-0.3254-0.0866-0.0414-0.0668-0.13340.00050.2333-0.01320.01630.2097-0.01610.225482.5179-24.9356-6.5263
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 64 )
2X-RAY DIFFRACTION2chain 'A' and (resid 65 through 92 )
3X-RAY DIFFRACTION3chain 'A' and (resid 93 through 153 )
4X-RAY DIFFRACTION4chain 'A' and (resid 154 through 245 )
5X-RAY DIFFRACTION5chain 'B' and (resid 5 through 64 )
6X-RAY DIFFRACTION6chain 'B' and (resid 65 through 236 )
7X-RAY DIFFRACTION7chain 'B' and (resid 237 through 247 )

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