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- PDB-5hje: Crystal Structure of Transketolase complex with sedoheptulose-7-p... -

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Basic information

Entry
Database: PDB / ID: 5hje
TitleCrystal Structure of Transketolase complex with sedoheptulose-7-phoaphate from Pichia Stipitis
ComponentsTransketolase
KeywordsTRANSFERASE / transketolase
Function / homology
Function and homology information


purine nucleotide metabolic process / transketolase / transketolase activity / metal ion binding
Similarity search - Function
Transketolase, bacterial-like / Transketolase family / Transketolase-like TK C-terminal domain / : / Transketolase signature 1. / Transketolase, thiamine diphosphate binding domain / Transketolase, N-terminal / Transketolase binding site / Transketolase signature 2. / Transketolase, C-terminal domain ...Transketolase, bacterial-like / Transketolase family / Transketolase-like TK C-terminal domain / : / Transketolase signature 1. / Transketolase, thiamine diphosphate binding domain / Transketolase, N-terminal / Transketolase binding site / Transketolase signature 2. / Transketolase, C-terminal domain / Rossmann fold - #920 / Transketolase-like, pyrimidine-binding domain / Transketolase, pyrimidine binding domain / Transketolase, pyrimidine binding domain / Transketolase C-terminal/Pyruvate-ferredoxin oxidoreductase domain II / Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains / Thiamin diphosphate-binding fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
D-ALTRO-HEPT-2-ULOSE 7-PHOSPHATE / THIAMINE DIPHOSPHATE / Transketolase
Similarity search - Component
Biological speciesScheffersomyces stipitis CBS 6054 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsLi, T.L. / Hsu, L.J. / Hsu, N.S.
CitationJournal: Protein Eng. Des. Sel. / Year: 2016
Title: Structural and biochemical interrogation on transketolase from Pichia stipitis for new functionality
Authors: Hsu, L.J. / Hsu, N.S. / Wang, Y.L. / Wu, C.J. / Li, T.L.
History
DepositionJan 13, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 25, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 5, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 8, 2023Group: 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

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Assembly

Deposited unit
A: Transketolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,8104
Polymers75,0541
Non-polymers7563
Water18,4831026
1
A: Transketolase
hetero molecules

A: Transketolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,6208
Polymers150,1092
Non-polymers1,5116
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area11820 Å2
ΔGint-73 kcal/mol
Surface area40910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.974, 183.201, 98.435
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
11A-844-

HOH

21A-928-

HOH

31A-1265-

HOH

41A-1658-

HOH

51A-1678-

HOH

61A-1774-

HOH

71A-1777-

HOH

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Components

#1: Protein Transketolase / TK


Mass: 75054.453 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Scheffersomyces stipitis CBS 6054 (fungus)
Strain: CBS 6054 / Gene: TKT, TKT1, PICST_67105 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P34736, transketolase
#2: Chemical ChemComp-TPP / THIAMINE DIPHOSPHATE


Mass: 425.314 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H19N4O7P2S
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-I22 / D-ALTRO-HEPT-2-ULOSE 7-PHOSPHATE / 7-O-PHOSPHONO-D-ALTRO-HEPT-2-ULOSE / SEDOHEPTULOSE 7-PHOSPHATE


Mass: 290.162 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C7H15O10P
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1026 / Source method: isolated from a natural source / Formula: H2O

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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: 3.03 Å3/Da / Density % sol: 59.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG400, MES, NaCl / PH range: 6.4-6.7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.7 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: May 11, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7 Å / Relative weight: 1
ReflectionResolution: 1.4→30 Å / Num. obs: 155291 / % possible obs: 86.8 % / Redundancy: 3.5 % / Biso Wilson estimate: 10.23 Å2 / Rmerge(I) obs: 0.08 / Net I/av σ(I): 12.493 / Net I/σ(I): 9.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.4-1.453.10.614181.1
1.45-1.513.20.481178.9
1.51-1.583.20.381179.2
1.58-1.663.10.304182.5
1.66-1.763.10.239185.1
1.76-1.930.191186.1
1.9-2.093.10.148190
2.09-2.393.90.106196.4
2.39-3.024.50.066194.9
3.02-3050.048193.4

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.10_2152: ???refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GPU

1gpu


Resolution: 1.4→29.477 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.82
RfactorNum. reflection% reflectionSelection details
Rfree0.1669 7810 5.03 %random selection
Rwork0.1496 ---
obs0.1505 155160 86.42 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 63.55 Å2 / Biso mean: 13.7648 Å2 / Biso min: 4.87 Å2
Refinement stepCycle: final / Resolution: 1.4→29.477 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5136 0 74 1026 6236
Biso mean--18.74 26.1 -
Num. residues----676
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115305
X-RAY DIFFRACTIONf_angle_d1.1867211
X-RAY DIFFRACTIONf_chiral_restr0.08806
X-RAY DIFFRACTIONf_plane_restr0.008933
X-RAY DIFFRACTIONf_dihedral_angle_d14.771893
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.3969-1.41280.26942010.24094054425572
1.4128-1.42940.23772240.22444615483981
1.4294-1.44680.24412330.21984556478980
1.4468-1.46510.21472340.2074472470679
1.4651-1.48440.22372640.20274403466779
1.4844-1.50470.21892360.20134448468479
1.5047-1.52620.24192650.1934411467679
1.5262-1.5490.21812290.18964463469279
1.549-1.57320.20772320.18764511474380
1.5732-1.5990.20542410.18124608484981
1.599-1.62660.18982440.17714647489182
1.6266-1.65620.20542440.17064757500184
1.6562-1.6880.17322630.16684773503684
1.688-1.72250.1862620.16614787504985
1.7225-1.75990.17472560.15914834509085
1.7599-1.80080.16092630.16314906516986
1.8008-1.84590.18942740.15744847512186
1.8459-1.89580.16352430.15534862510585
1.8958-1.95150.17172510.15364931518287
1.9515-2.01450.15882530.14845110536389
2.0145-2.08650.17082690.14255302557193
2.0865-2.170.15562890.13495428571796
2.17-2.26870.13392660.12665509577596
2.2687-2.38830.15282980.12115498579697
2.3883-2.53790.14663020.11995514581697
2.5379-2.73370.13823250.12755521584697
2.7337-3.00850.15442900.14065193548391
3.0085-3.44330.17112980.14295328562693
3.4433-4.3360.1332750.12875321559692
4.336-29.48370.16472860.15175741602796

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