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- PDB-1i2p: CRYSTAL STRUCTURE OF ESCHERICHIA COLI TRANSALDOLASE B MUTANT D17A -

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Basic information

Entry
Database: PDB / ID: 1i2p
TitleCRYSTAL STRUCTURE OF ESCHERICHIA COLI TRANSALDOLASE B MUTANT D17A
ComponentsTRANSALDOLASE B
KeywordsTRANSFERASE / alpha-beta barrel
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 / FOURIER SYNTHESIS / Resolution: 2.05 Å
AuthorsThorell, S. / Jia, J. / Schneider, G.
Citation
Journal: Eur.J.Biochem. / Year: 2001
Title: Identification of catalytically important residues in the active site of Escherichia coli transaldolase.
Authors: Schorken, U. / Thorell, S. / Schurmann, M. / Jia, J. / Sprenger, G.A. / Schneider, G.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1996
Title: Crystallization and Preliminary X-ray Analysis of Recombinant Transaldolase B from Escherichia coli
Authors: Jia, J. / Lindqvist, Y. / Schneider, G. / Schoerken, U. / Sahm, H. / Sprenger, G.A.
#2: 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. / Schoerken, U. / Sahm, H. / Sprenger, G.A. / Lindqvist, Y. / Schneider, G.
#3: 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. / Schoerken, U. / Lindqvist, Y. / Sprenger, G.A. / Schneider, G.
#4: Journal: FEBS Lett. / Year: 2000
Title: The Three-dimensional Structure of Human Transaldolase
Authors: Thorell, S. / Gergely Jr., P. / Banki, K. / Perl, A. / Schneider, G.
History
DepositionFeb 12, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 9, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Oct 27, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Aug 9, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)70,1682
Polymers70,1682
Non-polymers00
Water5,477304
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.381, 92.788, 131.537
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe dimer is generated with a symmetry molecule from one of the monomers in the asymmetric unit

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Components

#1: Protein TRANSALDOLASE B


Mass: 35083.953 Da / Num. of mol.: 2 / Mutation: D17A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: TALB / Plasmid: PGSJ451 / Production host: Escherichia coli (E. coli) / Strain (production host): LJ110 / References: UniProt: P0A870, transaldolase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 304 / 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: 3.02 Å3/Da / Density % sol: 59.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4
Details: PEG 6000, sodium citrate, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Details: used microseeding, Jia, J., (1996) Acta Crystallogr., Sect.D, 52, 192.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mg/mlprotein1drop
211-13 %(w/w)PEG60001reservoir
30.1 Msodium citrate1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 29, 1996
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.05→47.5 Å / Num. all: 49932 / Num. obs: 49932 / % possible obs: 92.4 % / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 17.5 Å2 / Rmerge(I) obs: 0.094 / Net I/σ(I): 13
Reflection shellResolution: 2.05→2.1 Å / Rmerge(I) obs: 0.344 / Mean I/σ(I) obs: 2.1 / Num. unique all: 3026 / % possible all: 85.4
Reflection
*PLUS
Num. measured all: 458342
Reflection shell
*PLUS
% possible obs: 85.4 %

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Processing

Software
NameClassification
CNSrefinement
MAR345data collection
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 1ONR

1onr


Resolution: 2.05→28.96 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2298834.19 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.221 2537 5.1 %RANDOM
Rwork0.193 ---
obs0.193 49929 92.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 51.33 Å2 / ksol: 0.317 e/Å3
Displacement parametersBiso mean: 32.8 Å2
Baniso -1Baniso -2Baniso -3
1-2.94 Å20 Å20 Å2
2--4.17 Å20 Å2
3----7.11 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.31 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 2.05→28.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4934 0 0 304 5238
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.7
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.131.5
X-RAY DIFFRACTIONc_mcangle_it1.772
X-RAY DIFFRACTIONc_scbond_it2.132
X-RAY DIFFRACTIONc_scangle_it3.192.5
LS refinement shellResolution: 2.05→2.18 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.297 366 4.7 %
Rwork0.298 7359 -
obs-7725 87.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 5.1 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 32.8 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg20.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.7
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.297 / % reflection Rfree: 4.7 % / Rfactor Rwork: 0.298 / Rfactor obs: 0.315

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