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- PDB-1ucw: COMPLEX OF TRANSALDOLASE WITH THE REDUCED SCHIFF-BASE INTERMEDIATE -

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Basic information

Entry
Database: PDB / ID: 1ucw
TitleCOMPLEX OF TRANSALDOLASE WITH THE REDUCED SCHIFF-BASE INTERMEDIATE
ComponentsTRANSALDOLASE
KeywordsTRANSFERASE / KETONE RESIDUES / PENTOSE SHUNT
Function / homology
Function and homology information


transketolase or transaldolase activity / transaldolase / transaldolase activity / pentose-phosphate shunt, non-oxidative branch / carbohydrate metabolic process / membrane / cytosol
Similarity search - Function
Transaldolase type 1 / Transaldolase active site. / Transaldolase, active site / Transaldolase signature 1. / Transaldolase/Fructose-6-phosphate aldolase / Transaldolase/Fructose-6-phosphate aldolase / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsJia, J. / Lindqvist, Y. / Schneider, G.
Citation
Journal: Protein Sci. / Year: 1997
Title: Crystal structure of the reduced Schiff-base intermediate complex of transaldolase B from Escherichia coli: mechanistic implications for class I aldolases.
Authors: Jia, J. / Schorken, U. / Lindqvist, Y. / Sprenger, G.A. / Schneider, G.
#1: Journal: Structure / Year: 1996
Title: Crystal Structure of Transaldolase B from Escherichia Coli Suggests a Circular Permutation of the Alpha/Beta Barrel within the Class I Aldolase Family
Authors: Jia, J. / Huang, W. / Schorken, U. / Sahm, H. / Sprenger, G.A. / Lindqvist, Y. / Schneider, G.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 1996
Title: Crystallization and Preliminary X-Ray Crystallographic Analysis of Recombinant Transaldolase B from Escherichia Coli
Authors: Jia, J. / Lindqvist, Y. / Schneider, G. / Schorken, U. / Sahm, H. / Sprenger, G.A.
History
DepositionNov 14, 1996Processing site: BNL
Revision 1.0Jul 7, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _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_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TRANSALDOLASE
B: TRANSALDOLASE


Theoretical massNumber of molelcules
Total (without water)70,7202
Polymers70,7202
Non-polymers00
Water9,098505
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.200, 91.900, 130.900
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: (1, -0.0067, 0.004), (0.0068, 0.9997, -0.0232), (-0.0039, 0.0232, 0.9997)
Vector: 0.4706, -45.227, 16.1575)

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Components

#1: Protein TRANSALDOLASE


Mass: 35360.199 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: THE LIGAND IS COVALENTLY BOUND TO THE SIDE CHAIN OF LYS 132
Source: (gene. exp.) Escherichia coli (E. coli) / Gene (production host): TALB / Production host: Escherichia coli (E. coli) / References: UniProt: P0A870, transaldolase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 505 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.94 Å3/Da / Density % sol: 51.6 %
Crystal grow
*PLUS
Temperature: 293 K / pH: 4 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.1 Msodium citrate1reservoir
215 %PEG60001reservoir

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Data collection

Diffraction sourceSource: SEALED TUBE / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 14, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 37868 / % possible obs: 87 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.099
Reflection shellResolution: 2.2→2.25 Å / % possible all: 77.5
Reflection
*PLUS
Highest resolution: 2.2 Å / Num. measured all: 173783
Reflection shell
*PLUS
% possible obs: 77.5 %

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
X-PLORphasing
RefinementResolution: 2.2→10 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.244 -5 %
Rwork0.204 --
obs0.204 37868 87 %
Displacement parametersBiso mean: 21.08 Å2
Refinement stepCycle: LAST / Resolution: 2.2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4958 0 0 505 5463
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.481
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCSNCS model details: TWO-FOLD SYMMETRY RESTRAINTS
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS

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