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- PDB-9ui2: Crystal structure of Thermus thermophilus HB8 transaldolase -

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Basic information

Entry
Database: PDB / ID: 9ui2
TitleCrystal structure of Thermus thermophilus HB8 transaldolase
ComponentsProbable transaldolase
KeywordsTRANSFERASE / nonulose / octulose / transaldolase / rare sugar
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
Probable transaldolase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsKamitori, S.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)22K04843 Japan
CitationJournal: J.Agric.Food Chem. / Year: 2025
Title: Synthetic Study of 8- and 9-Carbon Sugars by Transaldolase.
Authors: Yoshihara, A. / Miyoshi, E. / Tomino, S. / Hanaki, Y. / Mochizuki, S. / Yoshida, H. / Izumori, K. / Kamitori, S.
History
DepositionApr 15, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 30, 2025Provider: repository / Type: Initial release
Revision 1.1Aug 6, 2025Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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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
F: Probable transaldolase
G: Probable transaldolase
H: Probable transaldolase
I: Probable transaldolase
J: Probable transaldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)265,73456
Polymers262,23310
Non-polymers3,50146
Water26,6981482
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area54940 Å2
ΔGint-474 kcal/mol
Surface area74840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)173.380, 173.380, 422.580
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein
Probable transaldolase


Mass: 26223.264 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8) (bacteria)
Strain: ATCC 27634 / DSM 579 / HB8 / Gene: tal, TTHA1066 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5SJE8, transaldolase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: SO4
#3: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 27 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1482 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 3.5 Å3/Da / Density % sol: 64.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 1.26 M (NH4)SO4, 0.2 M LiSO4, 0.1 M Tris-HCl pH8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 15, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→49.75 Å / Num. obs: 402504 / % possible obs: 99.7 % / Redundancy: 20 % / CC1/2: 0.997 / Rmerge(I) obs: 0.12 / Net I/σ(I): 17.4
Reflection shellResolution: 1.7→1.74 Å / Mean I/σ(I) obs: 2.4 / Num. unique obs: 29603 / CC1/2: 0.89 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3S1V

3s1v


Resolution: 1.7→49.75 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.953 / SU B: 3.919 / SU ML: 0.063 / Cross valid method: THROUGHOUT / ESU R: 0.081 / ESU R Free: 0.081 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21109 20239 5 %RANDOM
Rwork0.18942 ---
obs0.19051 382265 99.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.653 Å2
Baniso -1Baniso -2Baniso -3
1-0.13 Å20.07 Å20 Å2
2--0.13 Å2-0 Å2
3----0.44 Å2
Refinement stepCycle: 1 / Resolution: 1.7→49.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17050 0 203 1482 18735
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0010.01217507
X-RAY DIFFRACTIONr_bond_other_d00.01617345
X-RAY DIFFRACTIONr_angle_refined_deg0.6931.82923738
X-RAY DIFFRACTIONr_angle_other_deg0.251.74239917
X-RAY DIFFRACTIONr_dihedral_angle_1_deg752240
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.8935110
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.729103000
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0350.22849
X-RAY DIFFRACTIONr_gen_planes_refined0.0010.0220150
X-RAY DIFFRACTIONr_gen_planes_other00.023550
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.3732.2138990
X-RAY DIFFRACTIONr_mcbond_other3.3732.2138990
X-RAY DIFFRACTIONr_mcangle_it4.3453.94811220
X-RAY DIFFRACTIONr_mcangle_other4.3453.94811221
X-RAY DIFFRACTIONr_scbond_it5.392.7478517
X-RAY DIFFRACTIONr_scbond_other5.392.7478518
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.3684.78812519
X-RAY DIFFRACTIONr_long_range_B_refined8.60523.4919867
X-RAY DIFFRACTIONr_long_range_B_other8.57322.2819483
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 1435 -
Rwork0.276 28129 -
obs--99.95 %
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)
10.22630.2264-0.0360.3738-0.06530.11030.0238-0.0373-0.00510.0366-0.00860.0188-0.0919-0.0655-0.01520.09180.0506-0.0190.05730.02430.072261.22955.7328122.9098
20.2479-0.0064-0.1490.0126-0.02870.31160.03990.0117-0.0147-0.0058-0.00490.0155-0.1523-0.0293-0.0350.15930.0392-0.02080.012-0.00210.071472.595967.81591.7017
30.0559-0.122-0.01370.31170.07960.17160.02370.0015-0.0115-0.06820.00430.0001-0.0209-0.0031-0.0280.09430.033-0.03660.0196-0.01450.090579.979439.93671.2952
40.0885-0.0101-0.00120.1175-0.12960.31350.0571-0.0063-0.0381-0.05090.00720.04640.0821-0.014-0.06440.09760.0059-0.06570.00650.00260.101473.154310.60489.8126
50.06070.01410.02810.1290.1150.35650.0216-0.0312-0.03310.01450.02150.01750.0184-0.0656-0.04310.0534-0.013-0.03670.0470.05050.109761.653820.3834121.751
60.13220.18040.06880.7275-0.1610.1935-0.0012-0.0749-0.03290.10050.05620.0653-0.0808-0.1466-0.0550.04860.06950.01420.16410.08070.097728.721847.6471115.2156
70.0329-0.1072-0.03730.37950.23580.58950.0002-0.0197-0.04410.0360.02980.10650.0971-0.1758-0.02990.0339-0.0492-0.04880.11790.08080.169432.816714.1087104.5736
80.0226-0.07480.03940.4102-0.43190.92650.0533-0.01-0.0375-0.16570.03590.11110.1569-0.1092-0.08930.1302-0.0265-0.130.04240.02080.147444.925514.642871.2865
90.1063-0.18590.0680.3551-0.16730.18890.0403-0.0038-0.0332-0.0340.04510.047-0.0006-0.0758-0.08540.09010.0579-0.0670.0721-0.00140.115448.629548.424961.4954
100.0917-0.05780.0890.0386-0.06190.1058-0.0266-0.0451-0.03940.01820.02550.0149-0.0464-0.04150.0010.1030.0907-0.02750.09980.01410.083138.098668.768188.2774
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-2 - 223
2X-RAY DIFFRACTION2B-2 - 223
3X-RAY DIFFRACTION3C-2 - 223
4X-RAY DIFFRACTION4D-2 - 223
5X-RAY DIFFRACTION5E-2 - 223
6X-RAY DIFFRACTION6F-1 - 223
7X-RAY DIFFRACTION7G-2 - 223
8X-RAY DIFFRACTION8H-2 - 223
9X-RAY DIFFRACTION9I-2 - 223
10X-RAY DIFFRACTION10J-2 - 223

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