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- PDB-7wrr: X-ray structure of Thermus thermophilus HB8 transketorase in comp... -

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Basic information

Entry
Database: PDB / ID: 7wrr
TitleX-ray structure of Thermus thermophilus HB8 transketorase in complex with TPP and MES
ComponentsTransketolase
KeywordsTRANSFERASE / transketolase / complex / TPP
Function / homology
Function and homology information


transketolase / transketolase activity / pentose-phosphate shunt / metal ion binding / cytosol
Similarity search - Function
Transketolase, bacterial-like / Transketolase family / : / Transketolase-like TK C-terminal domain / : / Transketolase signature 1. / Transketolase, N-terminal / Transketolase, thiamine diphosphate binding domain / Transketolase-like, pyrimidine-binding domain / Transketolase, pyrimidine binding domain ...Transketolase, bacterial-like / Transketolase family / : / Transketolase-like TK C-terminal domain / : / Transketolase signature 1. / Transketolase, N-terminal / Transketolase, thiamine diphosphate binding 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
THIAMINE DIPHOSPHATE / Transketolase
Similarity search - Component
Biological speciesThermus thermophilus HB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 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)299,56516
Polymers296,9234
Non-polymers2,64312
Water9,458525
1
A: Transketolase
B: Transketolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,7838
Polymers148,4612
Non-polymers1,3216
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9370 Å2
ΔGint-46 kcal/mol
Surface area41480 Å2
MethodPISA
2
C: Transketolase
D: Transketolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,7838
Polymers148,4612
Non-polymers1,3216
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9490 Å2
ΔGint-47 kcal/mol
Surface area41600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.720, 88.840, 117.610
Angle α, β, γ (deg.)72.564, 88.743, 73.740
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


Mass: 425.314 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C12H19N4O7P2S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H13NO4S / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 525 / 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: 2.42 Å3/Da / Density % sol: 49.09 %
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, 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 16, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.01→46.67 Å / Num. obs: 175041 / % possible obs: 97.7 % / Redundancy: 3.5 % / CC1/2: 0.997 / Net I/σ(I): 17.6
Reflection shellResolution: 2.01→2.06 Å / Num. unique obs: 12801 / CC1/2: 0.732

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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: 2.01→46.67 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.943 / SU B: 5.287 / SU ML: 0.139 / Cross valid method: FREE R-VALUE / ESU R: 0.205 / ESU R Free: 0.167
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2284 8735 4.99 %
Rwork0.1977 166306 -
all0.199 --
obs-175041 97.751 %
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: 43.074 Å2
Baniso -1Baniso -2Baniso -3
1-0.088 Å2-0.94 Å22.01 Å2
2---0.478 Å2-0.47 Å2
3----0.58 Å2
Refinement stepCycle: LAST / Resolution: 2.01→46.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20280 0 156 525 20961
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01320976
X-RAY DIFFRACTIONr_bond_other_d0.0010.01519896
X-RAY DIFFRACTIONr_angle_refined_deg1.6111.64828552
X-RAY DIFFRACTIONr_angle_other_deg1.351.57145752
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.39152596
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.11619.9651156
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.474153296
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.41115208
X-RAY DIFFRACTIONr_chiral_restr0.0770.22540
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0223688
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024864
X-RAY DIFFRACTIONr_nbd_refined0.2120.24888
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1910.219671
X-RAY DIFFRACTIONr_nbtor_refined0.1680.29946
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.29584
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.2793
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0420.29
X-RAY DIFFRACTIONr_metal_ion_refined0.1910.213
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1320.219
X-RAY DIFFRACTIONr_nbd_other0.1840.262
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2030.212
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1670.21
X-RAY DIFFRACTIONr_mcbond_it3.4714.36810396
X-RAY DIFFRACTIONr_mcbond_other3.4714.36710395
X-RAY DIFFRACTIONr_mcangle_it4.6516.53612988
X-RAY DIFFRACTIONr_mcangle_other4.6516.53712989
X-RAY DIFFRACTIONr_scbond_it3.694.76310580
X-RAY DIFFRACTIONr_scbond_other3.6864.76310578
X-RAY DIFFRACTIONr_scangle_it5.3727.00915564
X-RAY DIFFRACTIONr_scangle_other5.3727.00915565
X-RAY DIFFRACTIONr_lrange_it7.0452.06723567
X-RAY DIFFRACTIONr_lrange_other7.04152.06623516
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.01-2.0620.3376530.31112138X-RAY DIFFRACTION96.5723
2.062-2.1190.3216510.29211859X-RAY DIFFRACTION96.8416
2.119-2.180.3145840.26711608X-RAY DIFFRACTION97.0701
2.18-2.2470.2935270.24711277X-RAY DIFFRACTION97.1443
2.247-2.3210.2685840.22510962X-RAY DIFFRACTION97.2868
2.321-2.4020.2525820.21510582X-RAY DIFFRACTION97.4341
2.402-2.4930.2565370.20410213X-RAY DIFFRACTION97.5322
2.493-2.5950.2565070.2019886X-RAY DIFFRACTION97.6786
2.595-2.710.2355160.1999435X-RAY DIFFRACTION97.914
2.71-2.8420.2574770.2049020X-RAY DIFFRACTION98.0184
2.842-2.9960.2494520.2068627X-RAY DIFFRACTION98.2257
2.996-3.1770.2424310.2018222X-RAY DIFFRACTION98.2514
3.177-3.3960.2384070.2117647X-RAY DIFFRACTION98.5802
3.396-3.6680.2254040.2057179X-RAY DIFFRACTION98.6984
3.668-4.0180.213460.1866625X-RAY DIFFRACTION98.7814
4.018-4.4920.1653120.1555951X-RAY DIFFRACTION98.7388
4.492-5.1850.1762700.1535286X-RAY DIFFRACTION98.4932
5.185-6.3470.2062430.1784427X-RAY DIFFRACTION98.9197
6.347-8.9620.1741600.1513477X-RAY DIFFRACTION99.0738
8.962-46.670.169920.171886X-RAY DIFFRACTION98.0178

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