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- PDB-4rz6: Transaldolase B E96Q F178Y from E.coli -

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Basic information

Entry
Database: PDB / ID: 4rz6
TitleTransaldolase B E96Q F178Y from E.coli
ComponentsTransaldolase B
KeywordsTRANSFERASE / Tim barrel / homodimer / Transaldolase of Pentose phosphate pathway
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.802 Å
AuthorsStellmacher, L. / Sandalova, T. / Leptihn, S. / Schneider, G. / Sprenger, G.A. / Samland, A.K.
CitationJournal: ChemCatChem / Year: 2015
Title: Acid Base Catalyst Discriminates between a Fructose 6-Phosphate Aldolase and a Transaldolase
Authors: Stellmacher, L. / Sandalova, T. / Leptihn, S. / Schneider, G. / Sprenger, G.A. / Samland, A.K.
History
DepositionDec 18, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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 / 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

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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)75,76011
Polymers74,9512
Non-polymers8089
Water6,575365
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3560 Å2
ΔGint-106 kcal/mol
Surface area25050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.844, 89.513, 130.512
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.999999, -0.000809, -0.000882), (-0.000807, 0.999997, -0.00218), (0.000884, -0.002179, -0.999997)-67.92962, -0.12107, -49.08321

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Components

#1: Protein Transaldolase B


Mass: 37475.559 Da / Num. of mol.: 2 / Fragment: Transaldolase B / Mutation: E96Q, F178Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b0008, JW0007, talB, yaaK / Plasmid: pJF119 / Production host: Escherichia coli (E. coli)
Strain (production host): LJ110(DE3) talA- talB- pLysS RARE2
References: UniProt: P0A870, transaldolase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 365 / 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: 2.64 Å3/Da / Density % sol: 53.47 %
Crystal growTemperature: 293.2 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.15M (NH4)2SO4, 18% PEG 3350, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.2K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.072 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 13, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.072 Å / Relative weight: 1
ReflectionResolution: 1.8→54.07 Å / Num. all: 73150 / Num. obs: 73150 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 8.2
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 1.6 / Num. unique all: 10225 / % possible all: 95.6

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Processing

Software
NameVersionClassification
MxCuBEdata collection
MOLREPphasing
REFMAC5.8.0073refinement
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1ONR, monomer

1onr


Resolution: 1.802→54.07 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.945 / SU B: 9.125 / SU ML: 0.118 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.187 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24907 3676 5 %RANDOM
Rwork0.2008 ---
all0.20322 69409 --
obs0.20322 69409 98.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.327 Å2
Baniso -1Baniso -2Baniso -3
1-0.52 Å2-0 Å20 Å2
2--2.21 Å20 Å2
3----2.73 Å2
Refinement stepCycle: LAST / Resolution: 1.802→54.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4946 0 43 365 5354
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.025082
X-RAY DIFFRACTIONr_bond_other_d0.0050.024955
X-RAY DIFFRACTIONr_angle_refined_deg1.1581.9816885
X-RAY DIFFRACTIONr_angle_other_deg0.9963.00211412
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0815638
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.17225.043230
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.66515918
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.1771532
X-RAY DIFFRACTIONr_chiral_restr0.0590.2792
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025724
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021080
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.1032.9152534
X-RAY DIFFRACTIONr_mcbond_other3.0942.9132533
X-RAY DIFFRACTIONr_mcangle_it3.9334.3723166
X-RAY DIFFRACTIONr_mcangle_other3.9334.3743167
X-RAY DIFFRACTIONr_scbond_it3.2333.2412548
X-RAY DIFFRACTIONr_scbond_other3.2333.2412549
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.9514.7393716
X-RAY DIFFRACTIONr_long_range_B_refined4.91923.8486039
X-RAY DIFFRACTIONr_long_range_B_other4.91923.8486040
X-RAY DIFFRACTIONr_rigid_bond_restr2.1310037
X-RAY DIFFRACTIONr_sphericity_free41.6335148
X-RAY DIFFRACTIONr_sphericity_bonded12.598510190
LS refinement shellResolution: 1.802→1.849 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.402 239 -
Rwork0.344 4686 -
obs--91.19 %

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