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- PDB-3cwn: Escherichia coli transaldolase b mutant f178y -

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Basic information

Entry
Database: PDB / ID: 3cwn
TitleEscherichia coli transaldolase b mutant f178y
ComponentsTransaldolase B
KeywordsTRANSFERASE / transaldolase / aldolase / directed evolution / Cytoplasm / Pentose shunt
Function / homology
Function and homology information


transketolase or transaldolase activity / transaldolase / transaldolase activity / pentose-phosphate shunt, non-oxidative branch / pentose-phosphate shunt / 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
Transaldolase / Transaldolase B
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsSandalova, T. / Schneider, G. / Samland, A.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Replacement of a Phenylalanine by a Tyrosine in the Active Site Confers Fructose-6-phosphate Aldolase Activity to the Transaldolase of Escherichia coli and Human Origin.
Authors: Schneider, S. / Sandalova, T. / Schneider, G. / Sprenger, G.A. / Samland, A.K.
History
DepositionApr 22, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Aug 30, 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

Downloads & links

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Assembly

Deposited unit
A: Transaldolase B
B: Transaldolase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,3376
Polymers74,9532
Non-polymers3844
Water10,899605
1
A: Transaldolase B
hetero molecules

B: Transaldolase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,3376
Polymers74,9532
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_545-x,y-1/2,-z+1/21
Buried area2200 Å2
ΔGint-61 kcal/mol
Surface area25360 Å2
MethodPISA
2
B: Transaldolase B
hetero molecules

A: Transaldolase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,3376
Polymers74,9532
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y+1/2,-z+1/21
Unit cell
Length a, b, c (Å)65.864, 86.173, 131.191
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Transaldolase B


Mass: 37476.543 Da / Num. of mol.: 2 / Mutation: F178Y, A247T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: W3110 / Gene: talB, yaaK / Plasmid: pJF119EH / Production host: Escherichia coli (E. coli) / Strain (production host): XL1Blue
References: UniProt: P0A870, UniProt: K0BE10*PLUS, transaldolase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 605 / 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: 2.48 Å3/Da / Density % sol: 50.47 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 18 % PEG 3350, 0.2 M ammonium sulfate, 25 mM glycylglycine, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 26, 2007
RadiationMonochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 1.4→47 Å / Num. all: 135268 / Num. obs: 135268 / % possible obs: 92 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 10.2 Å2 / Rmerge(I) obs: 0.037 / Rsym value: 0.037 / Net I/σ(I): 21.4
Reflection shellResolution: 1.4→1.48 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.15 / Mean I/σ(I) obs: 5.7 / Num. unique all: 13203 / Rsym value: 0.15 / % possible all: 62

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DNAdata collection
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ONR

1onr


Resolution: 1.4→47 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.966 / SU B: 1.351 / SU ML: 0.025 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.06 / ESU R Free: 0.053 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17257 6756 5 %RANDOM
Rwork0.14892 ---
all0.15009 128434 --
obs0.15009 128434 91.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 9.546 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å20 Å2
2--0.4 Å20 Å2
3----0.46 Å2
Refinement stepCycle: LAST / Resolution: 1.4→47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5116 0 20 605 5741
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0225241
X-RAY DIFFRACTIONr_bond_other_d0.0010.023555
X-RAY DIFFRACTIONr_angle_refined_deg1.2121.9817148
X-RAY DIFFRACTIONr_angle_other_deg0.86338770
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3925695
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.3225.366246
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.03915976
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.7991532
X-RAY DIFFRACTIONr_chiral_restr0.070.2817
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025881
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02983
X-RAY DIFFRACTIONr_nbd_refined0.2290.21010
X-RAY DIFFRACTIONr_nbd_other0.1880.23853
X-RAY DIFFRACTIONr_nbtor_refined0.180.22575
X-RAY DIFFRACTIONr_nbtor_other0.0840.22656
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.130.2348
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3140.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.210.257
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1540.231
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.071.54303
X-RAY DIFFRACTIONr_mcbond_other0.3311.51309
X-RAY DIFFRACTIONr_mcangle_it1.25525254
X-RAY DIFFRACTIONr_scbond_it2.28532310
X-RAY DIFFRACTIONr_scangle_it3.1344.51861
X-RAY DIFFRACTIONr_rigid_bond_restr1.051310794
X-RAY DIFFRACTIONr_sphericity_free4.5713605
X-RAY DIFFRACTIONr_sphericity_bonded1.92938691
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.179 294 -
Rwork0.145 5869 -
obs-5869 57.18 %

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