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- PDB-1onr: STRUCTURE OF TRANSALDOLASE B -

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Basic information

Entry
Database: PDB / ID: 1onr
TitleSTRUCTURE OF TRANSALDOLASE B
ComponentsTRANSALDOLASE B
KeywordsTRANSFERASE / PENTOSE SHUNT / MULTIGENE FAMILY
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: 1.87 Å
AuthorsJia, J. / Huang, W. / Lindqvist, Y. / Schneider, G.
Citation
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.
#1: 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
DepositionAug 13, 1996Processing site: BNL
Revision 1.0Mar 12, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TRANSALDOLASE B
B: TRANSALDOLASE B


Theoretical massNumber of molelcules
Total (without water)70,2562
Polymers70,2562
Non-polymers00
Water9,440524
1
A: TRANSALDOLASE B


Theoretical massNumber of molelcules
Total (without water)35,1281
Polymers35,1281
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: TRANSALDOLASE B


Theoretical massNumber of molelcules
Total (without water)35,1281
Polymers35,1281
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.900, 91.300, 130.500
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, -0.0054, 0.003), (0.0054, 0.9997, -0.0231), (-0.0029, 0.0232, 0.9997)
Vector: 0.388, -45.2033, 16.1404)

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Components

#1: Protein TRANSALDOLASE B


Mass: 35127.965 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P0A870, transaldolase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 524 / 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: 2.92 Å3/Da / Density % sol: 51.6 %
Crystal grow
*PLUS
Temperature: 293 K / pH: 4 / Method: vapor diffusion, hanging drop / Details: Jia, J., (1996) Acta Crystallogr.,Sect.D, 52, 192.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.1 Msodium citrate1reservoir
215 %PEG60001reservoir
320 mg/mlenzyme1drop

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Jan 12, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 62509 / % possible obs: 91.3 % / Redundancy: 7 % / Rmerge(I) obs: 0.064
Reflection
*PLUS
Highest resolution: 1.87 Å / Num. measured all: 498214
Reflection shell
*PLUS
Highest resolution: 1.87 Å / Lowest resolution: 1.97 Å / % possible obs: 82.8 %

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementResolution: 1.87→5.5 Å
RfactorNum. reflection
Rfree0.234 -
Rwork0.201 -
obs0.201 59387
Displacement parametersBiso mean: 25.1 Å2
Refinement stepCycle: LAST / Resolution: 1.87→5.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4940 0 0 524 5464
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
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_deg1.506
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
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS

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