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- PDB-6ys0: Transaldolase variant D211A from T. acidophilum in complex with D... -

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Basic information

Entry
Database: PDB / ID: 6ys0
TitleTransaldolase variant D211A from T. acidophilum in complex with D-fructose 6-phosphate Schiff-base intermediate
ComponentsProbable transaldolase
KeywordsTRANSFERASE / ALPHA-BETA BARREL / CONFORMATIONAL SELECTION / DOMAIN SWAPPING / TIM BARREL / SCHIFF BASE / Large-scale motions / Substrate binding / rate-determining product release
Function / homology
Function and homology information


transaldolase / transaldolase activity / aldehyde-lyase activity / pentose-phosphate shunt / carbohydrate metabolic process / cytoplasm
Similarity search - Function
Transaldolase type 3B, putative / Transaldolase type 3B/Fructose-6-phosphate aldolase / Transaldolase/Fructose-6-phosphate aldolase, archaeal/bacterial / Transaldolase active site. / Transaldolase, active site / Transaldolase signature 1. / Transaldolase/Fructose-6-phosphate aldolase / Transaldolase/Fructose-6-phosphate aldolase / Aldolase-type TIM barrel
Similarity search - Domain/homology
ACETATE ION / FRUCTOSE -6-PHOSPHATE / Probable transaldolase
Similarity search - Component
Biological speciesThermoplasma acidophilum DSM 1728 (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsSautner, V. / Klaus, M. / Tittmann, K.
CitationJournal: To Be Published
Title: Large-scale motions underlie physical but not chemical steps in transaldolase mechanism: Substrate binding by conformational selection and rate-determining product release
Authors: Sautner, V. / Lietzow, T.H. / Klaus, M. / Funk, L.M. / Tittmann, K.
History
DepositionApr 20, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 12, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable transaldolase
B: Probable transaldolase
C: Probable transaldolase
D: Probable transaldolase
E: Probable transaldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,52622
Polymers122,2535
Non-polymers2,27417
Water7,548419
1
A: Probable transaldolase
B: Probable transaldolase
C: Probable transaldolase
D: Probable transaldolase
E: Probable transaldolase
hetero molecules

A: Probable transaldolase
B: Probable transaldolase
C: Probable transaldolase
D: Probable transaldolase
E: Probable transaldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)249,05344
Polymers244,50510
Non-polymers4,54734
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area51440 Å2
ΔGint-349 kcal/mol
Surface area74710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)148.002, 172.608, 99.309
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11C-303-

GOL

21C-304-

ACT

31C-304-

ACT

41C-498-

HOH

51E-404-

HOH

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Components

#1: Protein
Probable transaldolase


Mass: 24450.535 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoplasma acidophilum DSM 1728 (acidophilic)
Gene: tal, Ta0616 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q9HKI3, transaldolase
#2: Chemical
ChemComp-F6R / FRUCTOSE -6-PHOSPHATE


Mass: 260.136 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H13O9P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 419 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.59 Å3/Da / Density % sol: 52.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 188 mM ammonium acetate (pH 4.4), 10% (w/v) PEG 6000, and 25% (v/v) glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.7→65.142 Å / Num. obs: 137733 / % possible obs: 99 % / Redundancy: 13.69 % / Biso Wilson estimate: 36.08 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.032 / Rrim(I) all: 0.033 / Χ2: 1.034 / Net I/σ(I): 37.09 / Num. measured all: 1885581 / Scaling rejects: 129
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.7-1.814.0431.0743.21214060.911.11498.5
1.8-1.914.010.5495.83171120.9730.5798.4
1.9-214.1930.2810.7139810.9920.2999
2-313.7490.05239.375963110.05499.4
3-613.0160.02295.322243210.02399.8
6-1011.7620.02399.7125460.9990.02497.7
10-208.2310.02782.365580.9980.0383.8
20-506.5910.02772.62660.9980.0364.1
50-10040.02957.4710.03314.3

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3S0C

3s0c


Resolution: 1.7→65.142 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.2
RfactorNum. reflection% reflection
Rfree0.1975 6886 5 %
Rwork0.173 --
obs0.1742 137668 98.98 %
Solvent computationShrinkage radii: 1.2 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso max: 198.69 Å2 / Biso mean: 56.3768 Å2 / Biso min: 30.61 Å2
Refinement stepCycle: final / Resolution: 1.7→65.142 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8435 0 141 420 8996
Biso mean--51.69 53.1 -
Num. residues----1096
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.7-1.71930.3282260.3065429598
1.7193-1.73960.28742250.2926427898
1.7396-1.76080.29392280.2717431998
1.7608-1.78310.30692260.2663429399
1.7831-1.80650.28722260.2556429598
1.8065-1.83130.25662270.2241430498
1.8313-1.85740.2532260.2097428498
1.8574-1.88520.22582260.2005429998
1.8852-1.91460.24312280.1977431598
1.9146-1.9460.24052270.1908431499
1.946-1.97960.22412280.1888432199
1.9796-2.01560.22652280.1952434899
2.0156-2.05430.21552290.1877434799
2.0543-2.09630.23982280.1852434599
2.0963-2.14190.21842300.1841435799
2.1419-2.19170.20662290.1782435499
2.1917-2.24650.22512300.1763436299
2.2465-2.30720.19682290.16954356100
2.3072-2.37510.2042300.17224367100
2.3751-2.45180.20632300.17554366100
2.4518-2.53940.18992310.17244402100
2.5394-2.64110.2082320.1784399100
2.6411-2.76130.20692290.1874435599
2.7613-2.90690.17042320.1733440999
2.9069-3.0890.21852320.18044415100
3.089-3.32750.2252330.17854418100
3.3275-3.66240.2022350.17164460100
3.6624-4.19220.16812350.15064467100
4.1922-5.28140.16322360.1407447999
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)
11.476-1.04510.10123.77741.08430.6926-0.33150.3886-0.881-0.2517-0.23970.21812.0426-0.49830.36441.2424-0.15490.23550.5938-0.1970.82954.2427-72.8998-1.2707
22.8660.14271.75170.51861.06032.98230.6509-0.5276-1.1432-0.4708-0.5056-0.46671.71810.27210.0731.2450.03780.14550.5932-0.08560.89211.7947-73.078-4.789
32.287-0.435-0.7682.0259-1.92543.2894-0.37820.055-0.7813-0.9251-0.3476-0.46421.04170.4083-0.07771.5791-0.19420.38460.7676-0.39270.80749.1037-74.4607-13.3742
40.95230.1449-0.1362.4054-0.48851.5077-0.26290.5304-0.573-0.612-0.0215-0.20450.7912-0.37980.31850.6817-0.02910.10830.6228-0.19470.442111.5433-60.4847-14.7778
51.08350.23910.04091.82220.18433.15490.09730.56910.0082-0.60570.039-0.15770.12310.0072-0.02730.52620.04030.03260.5413-0.02630.391511.1938-51.7477-11.7517
61.322-0.2807-0.28371.2186-0.22840.76850.0040.0517-0.1754-0.0634-0.04480.00130.02950.10040.05840.37590.0039-0.01230.4263-0.05150.3919.6383-50.93333.6551
70.85690.5172-0.38971.1397-0.16750.4902-0.05080.0802-0.1093-0.1493-0.0421-0.01230.0384-0.07640.06770.3330.0164-0.01310.4171-0.06030.43724.1652-56.42985.8261
81.17750.7493-0.67751.8473-1.87482.5433-0.24330.1249-0.5401-0.77870.23340.2790.9568-0.31320.07280.5513-0.00550.02390.3896-0.09490.55583.3489-69.16267.8362
93.62950.3173-0.3133.8708-0.7314.29840.1521-0.3368-0.59170.4498-0.24021.31551.1615-0.93930.03340.8358-0.16240.08990.6842-0.04691.0593-11.9718-84.312523.0006
101.8472-0.4142-0.81661.9264-0.13012.44520.11090.2565-0.3112-0.1023-0.3041-0.31150.33460.46670.14680.68520.08380.08950.6280.02180.479317.6522-32.5634-11.2037
111.3246-0.66840.10661.5904-0.15882.2640.22250.38360.2512-0.3287-0.3191-0.56020.07780.60610.09620.67250.02230.11790.69550.0720.513420.8558-24.8764-11.2496
124.10151.95280.22453.4941-0.98192.03310.17560.9630.387-0.4651-0.1738-0.4471-0.5370.33590.04771.03790.13230.20970.73140.11760.52817.6097-22.1644-19.28
132.1863-0.9778-0.06464.0153-0.19530.38730.36110.33090.2157-0.2653-0.4878-0.1147-0.2346-0.3594-0.03660.73280.03320.09280.57670.08850.420810.8735-18.7071-10.3526
141.9753-0.5437-0.37782.73951.92473.27480.18380.4710.5105-1.14520.0338-0.064-0.89890.1619-0.07821.10950.09080.05180.63230.18410.54836.12-10.8907-14.0008
151.22-0.2963-0.08561.81630.25451.8070.18570.41810.2066-0.5381-0.03960.2543-0.5282-0.1131-0.17610.64780.0704-0.01230.47380.07520.40463.5655-16.3022-5.6803
161.3451-0.1187-0.40360.9953-0.00350.42950.08660.0510.0276-0.0592-0.0661-0.0463-0.1542-0.0039-0.03110.47920.0121-0.00230.39270.00520.33895.3636-25.04146.8613
171.2591-0.7734-0.57351.020.26150.63670.14840.20070.1261-0.1923-0.11890.04-0.1097-0.0492-0.0230.40820.003-0.02410.4054-0.00170.37417.3011-31.99433.4901
180.28390.09820.34562.4523-1.00121.0950.31650.2564-0.1034-0.5386-0.3079-0.49610.13160.3588-0.04810.47310.03870.04770.4815-0.00350.397217.2151-37.572-2.6238
191.8214-0.6892-0.13064.21052.39323.4499-0.07780.4574-0.6105-0.28460.1551-0.35290.6670.7646-0.00710.64550.10620.09470.6762-0.10590.696924.8878-62.3294-5.2476
202.16390.2892-0.14393.854-0.16670.9042-0.08460.42640.3183-0.23990.1062-0.1974-0.42250.07320.07240.70790.07260.01490.47510.11130.4951-8.3012-5.15648.2362
211.9538-0.07421.10351.4076-0.13172.4602-0.2022-0.16860.7454-0.09810.061-0.0208-1.16910.19480.08290.90110.1041-0.01840.40620.04580.5318-15.82131.468712.6554
221.05260.09-0.86652.0451-0.33111.61170.10210.080.1418-0.1725-0.00830.5713-0.6445-0.4018-0.06490.70420.2094-0.03340.50720.04590.5209-27.2016-6.917415.2715
231.3802-0.3934-0.11911.9615-0.20410.8817-0.01880.11490.1917-0.0570.0040.3689-0.2791-0.2815-0.02220.47160.1191-0.02360.49250.0280.4643-27.2697-17.326320.0017
241.83280.46271.17960.46320.43762.176-0.082-0.13050.3797-0.1455-0.06450.159-0.3475-0.0581-0.04030.53140.0751-0.01010.37660.030.3846-13.0829-16.601124.1856
251.59710.3381-0.35771.11220.06350.4380.03790.13520.0753-0.00180.0446-0.0562-0.1917-0.045-0.0840.48790.0434-0.00220.3910.0250.3318-8.5862-19.71516.6678
261.4545-0.0208-0.28640.62690.21832.96770.06260.6380.5787-0.6924-0.1404-0.5819-0.94370.79040.15780.9882-0.08420.08010.71850.16470.675719.2622-10.9387-4.6625
273.5105-0.0887-0.33720.96610.40023.0999-0.28860.00811.7238-0.1077-0.39891.3278-1.0009-0.82250.61910.62890.149-0.08920.6638-0.15941.1891-37.7779-26.933231.0359
283.54260.03591.41553.0886-0.53182.42490.0473-1.02450.69051.14-0.53981.0365-0.4666-0.41880.31290.60130.04570.08590.8676-0.19781.0216-45.5109-33.185735.5387
292.61360.7469-0.28362.0550.48471.6887-0.04850.11980.0773-0.16350.04390.51610.1003-0.4210.00990.32810.0165-0.0360.57060.02630.5649-43.9846-48.838228.5226
300.71080.13890.0361.0869-0.23460.57830.0594-0.0074-0.0656-0.0325-0.06070.0915-0.0283-0.1472-0.010.33950.0319-0.02460.4385-0.00210.3944-25.9586-43.92628.8689
311.92621.9441-0.09133.53640.61070.88460.1083-0.20680.50220.0342-0.34911.1139-0.4241-0.06790.0770.48340.0682-0.01260.481-0.02890.5016-28.0518-27.077131.738
320.21930.5233-0.19371.684-1.24943.21410.0170.17310.6604-0.036-0.2532-0.1937-1.5323-0.3041-0.06121.08810.2250.02740.5759-0.05020.6559-22.3795-0.470526.342
332.44940.4567-0.99051.1845-0.63512.6522-0.4168-0.6172-0.2120.3547-0.3371.18580.9108-1.23360.68590.6587-0.2170.2140.9888-0.31861.1807-30.203-69.187625.721
343.3053-2.17370.96951.75830.83758.2556-0.4304-1.1883-0.24960.1853-0.18890.25562.4156-0.93560.11540.904-0.24530.160.79-0.1351.2386-26.0439-78.622825.0225
351.14190.80690.33631.3349-0.34490.66460.2837-0.3131-0.36680.12310.27770.32390.4464-0.37610.83190.5396-0.96090.69650.8574-0.8822.0821-32.3072-80.872318.9759
361.8893-0.1562-0.61841.26630.31031.4738-0.04570.3961-0.7244-0.2878-0.43020.86250.3054-0.45530.30060.4504-0.0459-0.03650.5174-0.27720.8609-16.2194-76.03579.2874
370.5557-1.15-0.79771.46711.25572.188-0.09620.1903-0.31650.1117-0.12930.17960.0837-0.3480.22430.2882-0.0341-0.01560.3854-0.04690.4761-14.8717-62.031622.5011
386.1552-0.2536-0.47692.69830.41633.73830.0081-0.99380.75220.5122-0.36161.1425-0.8806-1.54210.23250.61370.05480.08130.9161-0.1360.7367-39.189-46.851644.1615
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 18 )A1 - 18
2X-RAY DIFFRACTION2chain 'A' and (resid 19 through 41 )A19 - 41
3X-RAY DIFFRACTION3chain 'A' and (resid 42 through 52 )A42 - 52
4X-RAY DIFFRACTION4chain 'A' and (resid 53 through 90 )A53 - 90
5X-RAY DIFFRACTION5chain 'A' and (resid 91 through 114 )A91 - 114
6X-RAY DIFFRACTION6chain 'A' and (resid 115 through 156 )A115 - 156
7X-RAY DIFFRACTION7chain 'A' and (resid 157 through 180 )A157 - 180
8X-RAY DIFFRACTION8chain 'A' and (resid 181 through 198 )A181 - 198
9X-RAY DIFFRACTION9chain 'A' and (resid 199 through 217 )A199 - 217
10X-RAY DIFFRACTION10chain 'B' and (resid 1 through 18 )B1 - 18
11X-RAY DIFFRACTION11chain 'B' and (resid 19 through 41 )B19 - 41
12X-RAY DIFFRACTION12chain 'B' and (resid 42 through 52 )B42 - 52
13X-RAY DIFFRACTION13chain 'B' and (resid 53 through 65 )B53 - 65
14X-RAY DIFFRACTION14chain 'B' and (resid 66 through 79 )B66 - 79
15X-RAY DIFFRACTION15chain 'B' and (resid 80 through 114 )B80 - 114
16X-RAY DIFFRACTION16chain 'B' and (resid 115 through 156 )B115 - 156
17X-RAY DIFFRACTION17chain 'B' and (resid 157 through 180 )B157 - 180
18X-RAY DIFFRACTION18chain 'B' and (resid 181 through 198 )B181 - 198
19X-RAY DIFFRACTION19chain 'B' and (resid 199 through 217 )B199 - 217
20X-RAY DIFFRACTION20chain 'C' and (resid 1 through 19 )C1 - 19
21X-RAY DIFFRACTION21chain 'C' and (resid 20 through 52 )C20 - 52
22X-RAY DIFFRACTION22chain 'C' and (resid 53 through 90 )C53 - 90
23X-RAY DIFFRACTION23chain 'C' and (resid 91 through 124 )C91 - 124
24X-RAY DIFFRACTION24chain 'C' and (resid 125 through 142 )C125 - 142
25X-RAY DIFFRACTION25chain 'C' and (resid 143 through 198 )C143 - 198
26X-RAY DIFFRACTION26chain 'C' and (resid 199 through 223 )C199 - 223
27X-RAY DIFFRACTION27chain 'D' and (resid 1 through 19 )D1 - 19
28X-RAY DIFFRACTION28chain 'D' and (resid 20 through 52 )D20 - 52
29X-RAY DIFFRACTION29chain 'D' and (resid 53 through 102 )D53 - 102
30X-RAY DIFFRACTION30chain 'D' and (resid 103 through 180 )D103 - 180
31X-RAY DIFFRACTION31chain 'D' and (resid 181 through 198 )D181 - 198
32X-RAY DIFFRACTION32chain 'D' and (resid 199 through 223 )D199 - 223
33X-RAY DIFFRACTION33chain 'E' and (resid 1 through 19 )E1 - 19
34X-RAY DIFFRACTION34chain 'E' and (resid 20 through 41 )E20 - 41
35X-RAY DIFFRACTION35chain 'E' and (resid 42 through 52 )E42 - 52
36X-RAY DIFFRACTION36chain 'E' and (resid 53 through 124 )E53 - 124
37X-RAY DIFFRACTION37chain 'E' and (resid 125 through 198 )E125 - 198
38X-RAY DIFFRACTION38chain 'E' and (resid 199 through 216 )E199 - 216

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