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- PDB-6yrt: Transaldolase variant T30D from T. acidophilum in complex with D-... -

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Basic information

Entry
Database: PDB / ID: 6yrt
TitleTransaldolase variant T30D from T. acidophilum in complex with D-fructose 6-phosphate Schiff-base intermediate
ComponentsTransaldolase
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 (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transaldolase
B: Transaldolase
C: Transaldolase
D: Transaldolase
E: Transaldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,81622
Polymers122,5435
Non-polymers2,27417
Water7,782432
1
A: Transaldolase
B: Transaldolase
C: Transaldolase
D: Transaldolase
E: Transaldolase
hetero molecules

A: Transaldolase
B: Transaldolase
C: Transaldolase
D: Transaldolase
E: Transaldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)249,63344
Polymers245,08510
Non-polymers4,54734
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area51000 Å2
ΔGint-365 kcal/mol
Surface area75170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)149.042, 172.522, 100.402
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-483-

HOH

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Components

#1: Protein
Transaldolase


Mass: 24508.529 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoplasma acidophilum (strain ATCC 25905 / DSM 1728 / JCM 9062 / NBRC 15155 / AMRC-C165) (acidophilic)
Strain: ATCC 25905 / DSM 1728 / JCM 9062 / NBRC 15155 / AMRC-C165
Gene: tal, Ta0616 / Production host: Escherichia coli BL21(DE3) (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.: 432 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.63 Å3/Da / Density % sol: 53.29 %
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: 1.65→112.784 Å / Num. obs: 153963 / % possible obs: 99.6 % / Redundancy: 13.561 % / Biso Wilson estimate: 35.15 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.039 / Rrim(I) all: 0.041 / Χ2: 1.067 / Net I/σ(I): 29.59 / Num. measured all: 2087960 / Scaling rejects: 102
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.65-1.7513.7611.1032.91247170.9131.14599.8
1.75-1.8513.9850.5395.57197180.9760.55999.8
1.85-1.9514.0570.2869.99159040.9920.29799.8
1.95-2.0513.9550.16216.14129920.9970.16999.8
2.05-313.5250.05139.995475810.05399.8
3-612.9090.03170.79228000.9990.03399.8
6-1011.2620.03268.6625190.9980.03394.9
10-207.2960.03653.344800.9950.0471.2
20-505.7390.03846.52690.9930.04267
50-1002.60.03933.8550.9960.04862.5

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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: 1.65→112.784 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22
RfactorNum. reflection% reflection
Rfree0.1866 7697 5 %
Rwork0.168 --
obs0.1689 153899 99.54 %
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.3 Å
Displacement parametersBiso max: 173.52 Å2 / Biso mean: 55.6463 Å2 / Biso min: 27.42 Å2
Refinement stepCycle: final / Resolution: 1.65→112.784 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8462 0 149 434 9045
Biso mean--49.41 52.26 -
Num. residues----1097
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.65-1.66880.32912530.29774796
1.6688-1.68840.28782550.26644850
1.6884-1.7090.25422550.2344844
1.709-1.73060.2582560.22674858
1.7306-1.75340.24932540.21774820
1.7534-1.77740.23582560.21134848
1.7774-1.80280.23652560.21014857
1.8028-1.82970.22182550.19074872
1.8297-1.85830.21832530.18684819
1.8583-1.88880.23942560.18044855
1.8888-1.92140.18312550.17834851
1.9214-1.95630.2172560.18094855
1.9563-1.99390.21182560.18324871
1.9939-2.03460.20212560.18484863
2.0346-2.07890.20852580.18444889
2.0789-2.12720.21252550.17954849
2.1272-2.18040.19752560.17674868
2.1804-2.23940.23262590.18014908
2.2394-2.30530.21392550.17674855
2.3053-2.37970.19862570.17524880
2.3797-2.46480.18242570.17464877
2.4648-2.56350.19222570.1714895
2.5635-2.68010.21322580.17644888
2.6801-2.82150.19342570.17924899
2.8215-2.99820.18962600.16654925
2.9982-3.22970.16822580.16864910
3.2297-3.55480.17722600.17294929
3.5548-4.06920.1762600.1474959
4.0692-5.12680.14922630.13244995
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)
12.7143-1.5886-0.11122.28761.45711.4772-0.23680.3686-0.8795-0.30420.0453-0.09051.7861-0.40390.06861.1234-0.13780.20580.4962-0.15820.66983.7203-73.1722-0.5764
25.7021-0.0714-0.52252.4441.20144.37650.2578-0.1361-0.6713-0.1359-0.2536-0.78571.48610.67570.02540.85440.16090.10230.5524-0.08020.612212.9165-72.8406-5.2004
32.09950.3507-0.27323.0113-0.15482.006-0.21060.4928-0.4157-0.6798-0.0285-0.22750.7177-0.1630.16130.6619-0.03120.12960.5969-0.1560.407711.5242-60.9214-14.0317
41.18240.2603-0.69460.9532-0.38771.5968-0.070.1099-0.1642-0.1406-0.0086-0.00660.1624-0.01520.07180.2984-0.01230.00490.34-0.06090.34077.3966-56.05853.8778
54.8221-0.56140.98873.51760.41615.70210.0665-0.4181-1.08160.2372-0.15160.79750.9927-0.96150.00020.7771-0.14950.07020.6448-0.02180.9846-11.559-84.009823.3328
61.62880.0888-1.12811.4259-0.20122.31890.23980.4712-0.091-0.4721-0.2576-0.4546-0.01280.5437-0.0310.66330.03040.13710.62320.0330.455417.8163-32.5424-10.7534
71.75360.22710.35693.6267-0.29782.18940.1090.64360.4112-0.5332-0.1499-0.76960.05370.9275-0.01770.68110.02720.19820.73720.12210.577121.1114-24.9165-10.9754
84.04811.30940.40612.7556-0.89511.4939-0.10470.68840.6387-0.4096-0.0962-0.4813-0.53220.6680.11141.07620.11940.22940.95010.21490.545917.8349-22.3783-19.1036
92.8914-0.9682-0.20044.05380.22821.59590.40090.5120.4083-0.1952-0.3134-0.1664-0.4537-0.2663-0.15340.8189-0.00870.12170.55140.110.39511.1154-18.7091-10.1668
102.196-0.8363-1.00823.58113.75984.02820.16050.47440.6447-0.66910.13580.099-0.6552-0.0334-0.2011.23910.08440.10570.66660.2380.59356.3058-10.9249-13.8982
111.0855-0.3822-0.27181.18190.08441.87210.24350.41450.2521-0.5513-0.02920.2422-0.5557-0.1058-0.20030.71540.06510.00550.45060.08930.41063.7655-16.276-5.4825
121.34450.0563-0.28680.93690.09890.80970.11010.1050.0371-0.1239-0.0344-0.0785-0.23650.0521-0.06660.4665-0.00080.00550.33990.00530.3355.6641-25.20897.3317
130.9424-0.7184-0.59581.14950.40250.72920.16190.20720.1386-0.1726-0.1133-0.0129-0.1677-0.0309-0.06690.3824-0.0051-0.01290.37130.00390.3287.5083-31.92793.7958
140.2441-0.17940.42192.3637-0.90620.87170.36380.3928-0.0395-0.6992-0.3504-0.47220.05310.3576-0.02490.44140.02290.08010.4944-0.00310.383517.4497-37.5149-2.2592
153.6060.14790.20684.48761.44064.43380.09131.0844-0.6706-0.6272-0.1867-0.58851.33280.43780.10870.75220.1470.10590.7633-0.14220.627125.135-62.417-4.718
161.3270.11-0.10254.0864-0.31291.0297-0.08280.40740.3965-0.32380.1347-0.3091-0.42020.3668-0.0070.80330.06780.02690.45170.13820.5238-8.1651-5.05098.3146
171.5034-0.1421-0.55691.3563-0.25931.8712-0.0401-0.09480.49550.00910.11460.315-0.7855-0.25780.01990.76050.2442-0.00070.42340.0780.5351-23.5688-4.573115.0319
181.27090.2556-0.41690.9099-0.04181.17660.06050.08050.2128-0.03080.0350.0662-0.312-0.1198-0.09380.4480.09140.00460.32360.04310.3339-12.6483-18.787319.1872
192.1405-0.35180.77410.20330.65384.4913-0.1070.6940.8504-1.01990.0093-0.6601-0.51481.30850.26321.0322-0.18190.16760.78030.20880.782319.4439-10.9926-3.7603
203.4188-0.8512-1.78670.98690.20273.2459-0.09650.07141.1607-0.0697-0.20511.2491-0.7545-0.76610.43650.490.1591-0.04740.671-0.09841.0385-38.113-27.491530.9771
213.03111.110.8065.1483-1.00713.3737-0.1786-1.09930.60710.9995-0.88980.6408-0.4737-0.84090.32480.56670.08970.00960.9839-0.21140.8386-42.6284-31.937636.8165
221.02380.7510.11411.75630.1791.12090.0309-0.03570.0922-0.055-0.04380.3596-0.086-0.3734-0.00720.25460.0609-0.02250.47360.01550.4108-33.6884-42.443329.1995
230.80480.48880.89510.9225-0.5574.9892-0.08230.23830.9257-0.0612-0.03010.2924-1.6205-0.65640.17221.08780.26410.04590.6391-0.03270.8824-21.8508-0.661327.0985
242.90351.2601-0.90011.6737-1.77472.0176-0.3923-0.3514-0.39250.0896-0.18921.11540.9181-1.29130.48350.5924-0.2690.22270.92-0.30521.0929-30.3292-68.999825.5389
253.6963-1.08291.0511.89120.79926.0238-0.3577-1.1107-0.82620.6813-0.15480.20921.9817-0.8083-0.10760.8673-0.32380.25830.7503-0.08321.0771-26.1382-78.580924.9598
261.02630.77450.32661.1225-0.09630.62430.2895-0.1506-0.31870.07610.03690.14570.172-0.12110.65140.756-0.61260.38751.0431-0.71251.6661-32.2844-80.765618.8024
271.307-0.6105-0.16451.14340.30421.308-0.06810.3666-0.5603-0.0841-0.21890.42740.4115-0.39190.21890.4172-0.11650.02970.448-0.18490.6477-14.912-74.411212.1421
280.7975-0.8919-0.9650.95550.90921.9711-0.1740.17-0.31160.0633-0.0410.14620.1328-0.42160.18020.2744-0.0423-0.00160.3838-0.03830.4225-15.8529-60.229722.4284
295.0887-1.30810.27976.0363-0.62574.6501-0.2075-0.81210.46250.6815-0.18121.2981-0.4399-1.58230.40240.52450.02180.1160.9778-0.14170.73-40.03-46.626244.189
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 19 )A1 - 19
2X-RAY DIFFRACTION2chain 'A' and (resid 20 through 41 )A20 - 41
3X-RAY DIFFRACTION3chain 'A' and (resid 42 through 102 )A42 - 102
4X-RAY DIFFRACTION4chain 'A' and (resid 103 through 198 )A103 - 198
5X-RAY DIFFRACTION5chain 'A' and (resid 199 through 217 )A199 - 217
6X-RAY DIFFRACTION6chain 'B' and (resid 1 through 18 )B1 - 18
7X-RAY DIFFRACTION7chain 'B' and (resid 19 through 41 )B19 - 41
8X-RAY DIFFRACTION8chain 'B' and (resid 42 through 52 )B42 - 52
9X-RAY DIFFRACTION9chain 'B' and (resid 53 through 65 )B53 - 65
10X-RAY DIFFRACTION10chain 'B' and (resid 66 through 79 )B66 - 79
11X-RAY DIFFRACTION11chain 'B' and (resid 80 through 114 )B80 - 114
12X-RAY DIFFRACTION12chain 'B' and (resid 115 through 156 )B115 - 156
13X-RAY DIFFRACTION13chain 'B' and (resid 157 through 180 )B157 - 180
14X-RAY DIFFRACTION14chain 'B' and (resid 181 through 198 )B181 - 198
15X-RAY DIFFRACTION15chain 'B' and (resid 199 through 217 )B199 - 217
16X-RAY DIFFRACTION16chain 'C' and (resid 1 through 19 )C1 - 19
17X-RAY DIFFRACTION17chain 'C' and (resid 20 through 102 )C20 - 102
18X-RAY DIFFRACTION18chain 'C' and (resid 103 through 198 )C103 - 198
19X-RAY DIFFRACTION19chain 'C' and (resid 199 through 223 )C199 - 223
20X-RAY DIFFRACTION20chain 'D' and (resid 1 through 18 )D1 - 18
21X-RAY DIFFRACTION21chain 'D' and (resid 19 through 41 )D19 - 41
22X-RAY DIFFRACTION22chain 'D' and (resid 42 through 198 )D42 - 198
23X-RAY DIFFRACTION23chain 'D' and (resid 199 through 223 )D199 - 223
24X-RAY DIFFRACTION24chain 'E' and (resid 1 through 19 )E1 - 19
25X-RAY DIFFRACTION25chain 'E' and (resid 20 through 41 )E20 - 41
26X-RAY DIFFRACTION26chain 'E' and (resid 42 through 52 )E42 - 52
27X-RAY DIFFRACTION27chain 'E' and (resid 53 through 142 )E53 - 142
28X-RAY DIFFRACTION28chain 'E' and (resid 143 through 198 )E143 - 198
29X-RAY DIFFRACTION29chain 'E' and (resid 199 through 217 )E199 - 217

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