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- PDB-1qgd: TRANSKETOLASE FROM ESCHERICHIA COLI -

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Basic information

Entry
Database: PDB / ID: 1qgd
TitleTRANSKETOLASE FROM ESCHERICHIA COLI
ComponentsPROTEIN (TRANSKETOLASE)
KeywordsTRANSFERASE / THIAMINE PYROPHOSPHATE / D-SEDOHEPTULOSE 7-PHOSPHATE D-GLYCERALDEHYDE 3- PHOSPHATE GLYCOLALDEHYDE TRANSFERASE
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
THIAMINE DIPHOSPHATE / Transketolase 1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsIsupov, M.N. / Littlechild, J.A.
Citation
Journal: To be Published
Title: Crystal Structure of Escherichia coli Transketolase
Authors: Isupov, M.N. / Rupprecht, M.P. / Wilson, K.S. / Dauter, Z. / Littlechild, J.A.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1995
Title: Crystallization and preliminary X-ray crystallographic data with Escherichia coli transketolase.
Authors: Littlechild, J. / Turner, N. / Hobbs, G. / Lilly, M. / Rawas, A. / Watson, H.
History
DepositionApr 23, 1999Deposition site: PDBE / Processing site: RCSB
Revision 1.0Jun 17, 2003Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 27, 2019Group: Data collection / Database references / Category: citation / diffrn_source
Item: _citation.pdbx_database_id_PubMed / _citation.title / _diffrn_source.pdbx_synchrotron_site
Revision 1.4Aug 16, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (TRANSKETOLASE)
B: PROTEIN (TRANSKETOLASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,3788
Polymers144,2552
Non-polymers1,1236
Water19,1861065
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10610 Å2
ΔGint-103 kcal/mol
Surface area40330 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)74.850, 126.000, 151.050
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.88878, 0.3481, -0.29816), (0.35265, 0.10385, -0.92997), (-0.29276, -0.93169, -0.21506)
Vector: 12.02042, 60.71593, 76.43806)

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Components

#1: Protein PROTEIN (TRANSKETOLASE)


Mass: 72127.430 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Cellular location: CYTOPLASM / Production host: Escherichia coli (E. coli) / References: UniProt: P27302, transketolase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-TPP / THIAMINE DIPHOSPHATE / Thiamine pyrophosphate


Mass: 425.314 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H19N4O7P2S
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1065 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsLYS A 105, SUGGESTED FROM ELECTRON DENSITY LYS B 105, SUGGESTED FROM ELECTRON DENSITY PRO A 585, ...LYS A 105, SUGGESTED FROM ELECTRON DENSITY LYS B 105, SUGGESTED FROM ELECTRON DENSITY PRO A 585, SUGGESTED FROM ELECTRON DENSITY PRO B 585, SUGGESTED FROM ELECTRON DENSITY

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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: 2.5 Å3/Da / Density % sol: 49 %
Crystal growpH: 6.4 / Details: pH 6.4

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.857
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 1, 1994
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.857 Å / Relative weight: 1
ReflectionResolution: 1.9→10 Å / Num. obs: 503703 / % possible obs: 98.2 % / Observed criterion σ(I): 0 / Redundancy: 4.68 % / Biso Wilson estimate: 23.6 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 16.3
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 3.29 % / Rmerge(I) obs: 0.323 / Mean I/σ(I) obs: 4.3 / % possible all: 97.1

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1TRK

1trk


Resolution: 1.9→10 Å / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.11 / ESU R Free: 0.11
RfactorNum. reflection% reflectionSelection details
Rfree0.176 2132 2 %RANDOM
Rwork0.132 ---
obs-104778 97.5 %-
Displacement parametersBiso mean: 18.2 Å2
Baniso -1Baniso -2Baniso -3
1-0.626 Å20 Å20 Å2
2--0.161 Å20 Å2
3----0.75 Å2
Refinement stepCycle: LAST / Resolution: 1.9→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10144 0 64 1065 11273
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0140.02
X-RAY DIFFRACTIONp_angle_d0.030.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0370.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.6844
X-RAY DIFFRACTIONp_mcangle_it3.1746
X-RAY DIFFRACTIONp_scbond_it5.9368
X-RAY DIFFRACTIONp_scangle_it8.00110
X-RAY DIFFRACTIONp_plane_restr0.0250.03
X-RAY DIFFRACTIONp_chiral_restr0.1490.15
X-RAY DIFFRACTIONp_singtor_nbd0.1710.3
X-RAY DIFFRACTIONp_multtor_nbd0.2470.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1540.3
X-RAY DIFFRACTIONp_planar_tor4.37
X-RAY DIFFRACTIONp_staggered_tor15.915
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor30.620
X-RAY DIFFRACTIONp_special_tor

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