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- PDB-5xtl: Crystal Structure of Transketolase in complex with aminopyrimidin... -

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Basic information

Entry
Database: PDB / ID: 5xtl
TitleCrystal Structure of Transketolase in complex with aminopyrimidine and cysteine sulfonic acid adduct from Pichia Stipitis
ComponentsTransketolase
KeywordsTRANSFERASE / transketolase
Function / homology
Function and homology information


transketolase / transketolase activity / pentose-phosphate shunt / metal ion binding / nucleus / cytosol
Similarity search - Function
Transketolase, bacterial-like / Transketolase family / : / Transketolase-like TK C-terminal domain / Transketolase, N-terminal / : / Transketolase, thiamine diphosphate binding domain / Transketolase signature 1. / Transketolase binding site / Transketolase signature 2. ...Transketolase, bacterial-like / Transketolase family / : / Transketolase-like TK C-terminal domain / Transketolase, N-terminal / : / Transketolase, thiamine diphosphate binding domain / Transketolase signature 1. / 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
2-methylpyrimidin-4-amine / PROPYL TRIHYDROGEN DIPHOSPHATE / DI(HYDROXYETHYL)ETHER / Transketolase
Similarity search - Component
Biological speciesScheffersomyces stipitis CBS 6054 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.101 Å
AuthorsLi, T.L. / Hsu, N.S. / Wang, Y.L.
CitationJournal: Angew. Chem. Int. Ed. Engl. / Year: 2018
Title: The Mesomeric Effect of Thiazolium on non-Kekule Diradicals in Pichia stipitis Transketolase.
Authors: Hsu, N.S. / Wang, Y.L. / Lin, K.H. / Chang, C.F. / Lyu, S.Y. / Hsu, L.J. / Liu, Y.C. / Chang, C.Y. / Wu, C.J. / Li, T.L.
History
DepositionJun 20, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 25, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transketolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,7907
Polymers75,1021
Non-polymers6886
Water15,835879
1
A: Transketolase
hetero molecules

A: Transketolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,58014
Polymers150,2052
Non-polymers1,37512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area11430 Å2
ΔGint-71 kcal/mol
Surface area41460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.578, 186.086, 98.835
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-819-

HOH

21A-959-

HOH

31A-1183-

HOH

41A-1483-

HOH

51A-1578-

HOH

61A-1594-

HOH

71A-1660-

HOH

81A-1676-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Transketolase / TK


Mass: 75102.453 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 / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: P34736, transketolase

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Non-polymers , 5 types, 885 molecules

#2: Chemical ChemComp-P23 / PROPYL TRIHYDROGEN DIPHOSPHATE


Mass: 220.055 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H10O7P2
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-8GF / 2-methylpyrimidin-4-amine / 2-methyl-4-aminopyrimidine


Mass: 109.129 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H7N3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 879 / 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: 3.11 Å3/Da / Density % sol: 60.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1M MES, 0.1M NaCl, PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jan 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.1→30 Å / Num. obs: 369681 / % possible obs: 98.9 % / Redundancy: 8.4 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 15.6
Reflection shellResolution: 1.1→1.14 Å / Rmerge(I) obs: 0.48

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HYV

5hyv


Resolution: 1.101→27.622 Å / SU ML: 0.07 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 15.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.171 18299 4.96 %
Rwork0.1615 --
obs0.162 368846 98.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.101→27.622 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5132 0 42 879 6053
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085428
X-RAY DIFFRACTIONf_angle_d1.0967405
X-RAY DIFFRACTIONf_dihedral_angle_d6.5123109
X-RAY DIFFRACTIONf_chiral_restr0.091825
X-RAY DIFFRACTIONf_plane_restr0.008967
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1006-1.11310.22415650.200610979X-RAY DIFFRACTION93
1.1131-1.12620.21196140.187311724X-RAY DIFFRACTION100
1.1262-1.13990.19436230.178311761X-RAY DIFFRACTION99
1.1399-1.15440.18636180.170511644X-RAY DIFFRACTION100
1.1544-1.16960.18586190.168711797X-RAY DIFFRACTION100
1.1696-1.18560.18565990.16111761X-RAY DIFFRACTION100
1.1856-1.20250.17836530.159911741X-RAY DIFFRACTION100
1.2025-1.22050.1756010.156711809X-RAY DIFFRACTION100
1.2205-1.23950.17166280.154811800X-RAY DIFFRACTION100
1.2395-1.25990.17036670.15411725X-RAY DIFFRACTION100
1.2599-1.28160.17086110.149111767X-RAY DIFFRACTION100
1.2816-1.30490.16186150.14711759X-RAY DIFFRACTION100
1.3049-1.330.16056490.147611786X-RAY DIFFRACTION100
1.33-1.35710.15556140.146111793X-RAY DIFFRACTION100
1.3571-1.38660.16475860.144211819X-RAY DIFFRACTION100
1.3866-1.41890.15786130.143911834X-RAY DIFFRACTION100
1.4189-1.45440.15946610.142411747X-RAY DIFFRACTION100
1.4544-1.49370.15516080.131911856X-RAY DIFFRACTION100
1.4937-1.53760.15426210.13711748X-RAY DIFFRACTION100
1.5376-1.58730.14855710.134811818X-RAY DIFFRACTION100
1.5873-1.6440.14946440.136311762X-RAY DIFFRACTION99
1.644-1.70980.15715910.136911826X-RAY DIFFRACTION99
1.7098-1.78760.14925960.139311798X-RAY DIFFRACTION99
1.7876-1.88180.15695610.144510712X-RAY DIFFRACTION90
1.8818-1.99970.17445100.172410411X-RAY DIFFRACTION87
1.9997-2.15410.20166100.192611903X-RAY DIFFRACTION100
2.1541-2.37070.18936150.181711928X-RAY DIFFRACTION100
2.3707-2.71350.18296180.175311947X-RAY DIFFRACTION100
2.7135-3.41770.17635670.171412026X-RAY DIFFRACTION99
3.4177-27.63110.16236510.153311566X-RAY DIFFRACTION94

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