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- PDB-7wrt: X-ray structure ofThermus thermophilus HB8 transketorase demonstr... -

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Basic information

Entry
Database: PDB / ID: 7wrt
TitleX-ray structure ofThermus thermophilus HB8 transketorase demonstrate in complex with TPP and D-erythrose-4-phosphate
ComponentsTransketolase
KeywordsTRANSFERASE / transketolase / complex / TPP / D-erythrose-4-phosphate
Function / homology
Function and homology information


transketolase / transketolase activity / metal ion binding
Similarity search - Function
Transketolase, bacterial-like / Transketolase family / : / Transketolase, thiamine diphosphate binding domain / Transketolase signature 1. / Transketolase, N-terminal / Transketolase, C-terminal domain / Transketolase, C-terminal domain / Transketolase-like, pyrimidine-binding domain / Transketolase, pyrimidine binding domain ...Transketolase, bacterial-like / Transketolase family / : / Transketolase, thiamine diphosphate binding domain / Transketolase signature 1. / Transketolase, N-terminal / Transketolase, C-terminal domain / Transketolase, C-terminal domain / Transketolase-like, pyrimidine-binding domain / Transketolase, pyrimidine binding domain / Transketolase, pyrimidine binding domain / Transketolase C-terminal/Pyruvate-ferredoxin oxidoreductase domain II / Thiamin diphosphate-binding fold
Similarity search - Domain/homology
ERYTHOSE-4-PHOSPHATE / THIAMINE DIPHOSPHATE / transketolase
Similarity search - Component
Biological speciesThermus thermophilus HB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsKamitori, S. / Yoshihara, A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Appl.Microbiol.Biotechnol. / Year: 2023
Title: Structural and biochemical characterizations of Thermus thermophilus HB8 transketolase producing a heptulose.
Authors: Yoshihara, A. / Takamatsu, Y. / Mochizuki, S. / Yoshida, H. / Masui, R. / Izumori, K. / Kamitori, S.
History
DepositionJan 27, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 7, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transketolase
B: Transketolase
C: Transketolase
D: Transketolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)299,58516
Polymers296,9234
Non-polymers2,66212
Water3,297183
1
A: Transketolase
B: Transketolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,7928
Polymers148,4612
Non-polymers1,3316
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9460 Å2
ΔGint-45 kcal/mol
Surface area41420 Å2
MethodPISA
2
C: Transketolase
D: Transketolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,7928
Polymers148,4612
Non-polymers1,3316
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9560 Å2
ΔGint-48 kcal/mol
Surface area41880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.680, 88.860, 117.370
Angle α, β, γ (deg.)72.308, 88.696, 73.459
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Transketolase /


Mass: 74230.727 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus HB8 (bacteria) / Gene: TTHA0108 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5SM35, transketolase
#2: Chemical
ChemComp-TPP / THIAMINE DIPHOSPHATE / Thiamine pyrophosphate


Mass: 425.314 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H19N4O7P2S
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Sugar
ChemComp-E4P / ERYTHOSE-4-PHOSPHATE / Erythrose 4-phosphate


Type: saccharideCarbohydrate / Mass: 200.084 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H9O7P
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 183 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.33 Å3/Da / Density % sol: 47.12 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 100mM imidazole/MES buffer pH 6.5, 20%(v/v) ethylene glycol, 10% (w/v) PEG 8000, 24mM of D-glucose, D-mannose, D-galactose, L-fucose, D-xylose, and N-acetyl-D-glucosamine

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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: May 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.25→41.86 Å / Num. obs: 124659 / % possible obs: 98.1 % / Redundancy: 3.5 % / CC1/2: 0.998 / Net I/σ(I): 18.6
Reflection shellResolution: 2.25→2.31 Å / Num. unique obs: 9119 / CC1/2: 0.839

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2E6K

2e6k


Resolution: 2.25→41.86 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.935 / WRfactor Rfree: 0.231 / WRfactor Rwork: 0.18 / SU B: 9.404 / SU ML: 0.221 / Average fsc free: 0.8578 / Average fsc work: 0.8747 / Cross valid method: FREE R-VALUE / ESU R: 0.352 / ESU R Free: 0.244
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.254 6251 5.014 %
Rwork0.202 118408 -
all0.205 --
obs-124659 98.152 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 55.66 Å2
Baniso -1Baniso -2Baniso -3
1--0.409 Å2-0.111 Å20.005 Å2
2--0.057 Å2-0.084 Å2
3---0.172 Å2
Refinement stepCycle: LAST / Resolution: 2.25→41.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20280 0 156 183 20619
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01320972
X-RAY DIFFRACTIONr_bond_other_d0.0010.01519864
X-RAY DIFFRACTIONr_angle_refined_deg1.6421.65128548
X-RAY DIFFRACTIONr_angle_other_deg1.2561.57345672
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.71252596
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.72719.9651156
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.407153296
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.54615208
X-RAY DIFFRACTIONr_chiral_restr0.0720.22548
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0223700
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024868
X-RAY DIFFRACTIONr_nbd_refined0.2120.25071
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1870.219966
X-RAY DIFFRACTIONr_nbtor_refined0.1660.29808
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.210107
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1670.2631
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1040.214
X-RAY DIFFRACTIONr_metal_ion_refined0.1740.29
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1110.212
X-RAY DIFFRACTIONr_nbd_other0.1610.259
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1830.23
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0020.21
X-RAY DIFFRACTIONr_mcbond_it5.1855.70810396
X-RAY DIFFRACTIONr_mcbond_other5.1855.70810395
X-RAY DIFFRACTIONr_mcangle_it7.2398.54412988
X-RAY DIFFRACTIONr_mcangle_other7.2398.54512989
X-RAY DIFFRACTIONr_scbond_it5.0136.13610576
X-RAY DIFFRACTIONr_scbond_other5.0136.13610576
X-RAY DIFFRACTIONr_scangle_it7.2379.05415560
X-RAY DIFFRACTIONr_scangle_other7.2379.05415561
X-RAY DIFFRACTIONr_lrange_it9.75267.78923447
X-RAY DIFFRACTIONr_lrange_other9.75267.78923443
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.25-2.3080.3444360.32286530.32393560.6970.71397.14620.286
2.308-2.3710.3484370.29984890.30191530.7480.76797.51990.258
2.371-2.440.3324530.2882590.28289260.7940.80997.60250.238
2.44-2.5150.3084410.25179370.25485730.8360.84997.72540.211
2.515-2.5970.3093970.24378420.24784240.8470.86997.80390.202
2.597-2.6880.3184270.25375030.25780990.8250.85797.91330.211
2.688-2.7890.33940.24972420.25277840.860.86598.09870.209
2.789-2.9020.2953670.23970060.24274990.8580.87898.31980.199
2.902-3.030.33530.22567580.22872260.8670.89998.40850.189
3.03-3.1770.2913430.2264550.22369180.8850.90898.26540.191
3.177-3.3480.2863240.21461080.21865160.8880.91898.71090.192
3.348-3.550.2752900.21658160.21961940.9050.92298.57930.201
3.55-3.7930.2472920.20254550.20558210.9280.93898.72870.189
3.793-4.0940.2272490.18251390.18454500.9380.94998.86240.173
4.094-4.480.2072550.16146650.16349750.9440.95498.89450.157
4.48-5.0020.2092310.15942330.16245240.9550.96298.67370.158
5.002-5.7620.2181930.16637420.16840000.9550.96198.3750.162
5.762-7.0240.2321740.17231870.17533910.9450.95199.11530.173
7.024-9.7970.1721320.14124900.14226400.9610.96699.31820.154
9.797-41.860.209630.1814290.18115190.9360.9598.22250.205

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