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- PDB-2r5n: Crystal structure of transketolase from Escherichia coli in nonco... -

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Basic information

Entry
Database: PDB / ID: 2r5n
TitleCrystal structure of transketolase from Escherichia coli in noncovalent complex with acceptor aldose ribose 5-phosphate
ComponentsTransketolase 1
KeywordsTRANSFERASE / thiamin catalysis / sugar phosphates / acceptor / near attack conformation / cyclic / acyclic / ribose-5-phospate / pyranose / Metal-binding / Thiamine pyrophosphate
Function / homology
Function and homology information


transketolase / transketolase activity / pentose-phosphate shunt, non-oxidative branch / pentose-phosphate shunt / thiamine pyrophosphate binding / manganese ion binding / magnesium ion binding / protein homodimerization activity / cytosol
Similarity search - Function
Transketolase, bacterial-like / Transketolase family / : / Transketolase signature 1. / Transketolase, thiamine diphosphate binding domain / Transketolase binding site / Transketolase signature 2. / Transketolase, N-terminal / Transketolase, C-terminal domain / Transketolase, C-terminal domain ...Transketolase, bacterial-like / Transketolase family / : / Transketolase signature 1. / Transketolase, thiamine diphosphate binding domain / Transketolase binding site / Transketolase signature 2. / Transketolase, N-terminal / Transketolase, C-terminal domain / 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
RIBOSE-5-PHOSPHATE / 5-O-phosphono-beta-D-ribofuranose / THIAMINE DIPHOSPHATE / Transketolase 1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å
AuthorsParthier, C. / Asztalos, P. / Wille, G. / Tittmann, K.
CitationJournal: Biochemistry / Year: 2007
Title: Strain and Near Attack Conformers in Enzymic Thiamin Catalysis: X-ray Crystallographic Snapshots of Bacterial Transketolase in Covalent Complex with Donor Ketoses Xylulose 5-phosphate and ...Title: Strain and Near Attack Conformers in Enzymic Thiamin Catalysis: X-ray Crystallographic Snapshots of Bacterial Transketolase in Covalent Complex with Donor Ketoses Xylulose 5-phosphate and Fructose 6-phosphate, and in Noncovalent Complex with Acceptor Aldose Ribose 5-phosphate.
Authors: Asztalos, P. / Parthier, C. / Golbik, R. / Kleinschmidt, M. / Hubner, G. / Weiss, M.S. / Friedemann, R. / Wille, G. / Tittmann, K.
History
DepositionSep 4, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp ...atom_site / chem_comp / pdbx_chem_comp_identifier / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.mon_nstd_flag / _chem_comp.type / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_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_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transketolase 1
B: Transketolase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,85725
Polymers146,2432
Non-polymers2,61423
Water29,3281628
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.969, 101.738, 132.859
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Transketolase 1 / / TK 1


Mass: 73121.508 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: tktA, tkt / Plasmid: pGSJ427 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P27302, transketolase

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Sugars , 2 types, 3 molecules

#2: Sugar ChemComp-R5P / RIBOSE-5-PHOSPHATE / Ribose 5-phosphate


Type: saccharideCarbohydrate / Mass: 230.110 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C5H11O8P
#6: Sugar ChemComp-RP5 / 5-O-phosphono-beta-D-ribofuranose / [(2R,3S,4S,5R)-3,4,5-TRIHYDROXYTETRAHYDROFURAN-2-YL]METHYL DIHYDROGEN PHOSPHATE / 5-O-phosphono-beta-D-ribose / 5-O-phosphono-D-ribose / 5-O-phosphono-ribose


Type: D-saccharide, beta linking / Mass: 230.110 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H11O8P
IdentifierTypeProgram
b-D-Ribf5PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 4 types, 1648 molecules

#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-TPP / THIAMINE DIPHOSPHATE / Thiamine pyrophosphate


Mass: 425.314 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H19N4O7P2S
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1628 / 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: 2.08 Å3/Da / Density % sol: 40.83 %
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop / pH: 7.9
Details: 50 mM glycyl-glycine, 10 mM thiamin diphosphate, 5 mM calcium chloride, 19-22% PEG6000, 1% glycerol, pH 7.9, VAPOR DIFFUSION, HANGING DROP, temperature 281K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Feb 28, 2007 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.5→35 Å / Num. all: 184035 / Num. obs: 184180 / % possible obs: 94.7 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 12.1 % / Biso Wilson estimate: 23.5 Å2 / Rmerge(I) obs: 0.111 / Rsym value: 0.111 / Net I/σ(I): 4.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.5-1.585.30.9880.8102029191930.98868.7
1.58-1.6810.50.6261.2268454255640.62696.1
1.68-1.7913.20.4051.9330381249650.40599.5
1.79-1.9413.10.2493303793232260.24999.2
1.94-2.1212.90.1644.4276828215110.16499.7
2.12-2.3712.80.1126.2250137195650.112100
2.37-2.7413.20.0867.8227832173250.086100
2.74-3.3514.20.087.6209618147500.08100
3.35-4.7414.70.0688.1169032115290.068100
4.74-44.2814.20.0717.19278165520.07199.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 0.351 / Cor.coef. Fo:Fc: 0.668 / Cor.coef. Io to Ic: 0.484
Highest resolutionLowest resolution
Rotation3 Å25 Å
Translation3 Å25 Å

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Processing

Software
NameVersionClassificationNB
d*TREKdata scaling
SCALAdata scaling
AMoREphasing
REFMACrefinement
PDB_EXTRACT3data extraction
CrystalCleardata collection
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1QGD

1qgd


Resolution: 1.6→35 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.951 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.09 / ESU R Free: 0.09 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: The ligand ribose-5-phosphate (chain ID C) is present in two different chemical entities: in cyclic (RP5) and acyclic (R5P) form, each with partial occupancy (0.25). The coordinates of R5P ...Details: The ligand ribose-5-phosphate (chain ID C) is present in two different chemical entities: in cyclic (RP5) and acyclic (R5P) form, each with partial occupancy (0.25). The coordinates of R5P and RP5 of chain C overlap in the structure since they have been refined independently from each other.
RfactorNum. reflection% reflectionSelection details
Rfree0.196 8028 5 %RANDOM
Rwork0.163 ---
all0.169 160722 --
obs0.164 159774 99.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.34 Å2
Baniso -1Baniso -2Baniso -3
1--0.41 Å20 Å20 Å2
2--0.06 Å20 Å2
3---0.35 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.09 Å0.09 Å
Refinement stepCycle: LAST / Resolution: 1.6→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10198 0 160 1628 11986
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02210633
X-RAY DIFFRACTIONr_angle_refined_deg1.231.95814403
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.62351343
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.57824.277477
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.503151699
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4611556
X-RAY DIFFRACTIONr_chiral_restr0.0870.21545
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.028144
X-RAY DIFFRACTIONr_nbd_refined0.1970.25803
X-RAY DIFFRACTIONr_nbtor_refined0.3050.27281
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1090.21414
X-RAY DIFFRACTIONr_metal_ion_refined0.1350.210
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1670.272
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0970.278
X-RAY DIFFRACTIONr_mcbond_it0.5061.56618
X-RAY DIFFRACTIONr_mcangle_it0.867210546
X-RAY DIFFRACTIONr_scbond_it1.63434015
X-RAY DIFFRACTIONr_scangle_it2.5334.53851
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.43 624 -
Rwork0.348 10734 -
all-11358 -
obs--96.34 %

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