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- PDB-1f05: CRYSTAL STRUCTURE OF HUMAN TRANSALDOLASE -

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Basic information

Entry
Database: PDB / ID: 1f05
TitleCRYSTAL STRUCTURE OF HUMAN TRANSALDOLASE
ComponentsTRANSALDOLASE
KeywordsTRANSFERASE / alpha-beta barrel
Function / homology
Function and homology information


xylulose biosynthetic process / TALDO1 deficiency: failed conversion of SH7P, GA3P to Fru(6)P, E4P / TALDO1 deficiency: failed conversion of Fru(6)P, E4P to SH7P, GA3P / glyceraldehyde-3-phosphate metabolic process / Insulin effects increased synthesis of Xylulose-5-Phosphate / transaldolase / transaldolase activity / Pentose phosphate pathway / pentose-phosphate shunt, non-oxidative branch / pentose-phosphate shunt ...xylulose biosynthetic process / TALDO1 deficiency: failed conversion of SH7P, GA3P to Fru(6)P, E4P / TALDO1 deficiency: failed conversion of Fru(6)P, E4P to SH7P, GA3P / glyceraldehyde-3-phosphate metabolic process / Insulin effects increased synthesis of Xylulose-5-Phosphate / transaldolase / transaldolase activity / Pentose phosphate pathway / pentose-phosphate shunt, non-oxidative branch / pentose-phosphate shunt / fructose 6-phosphate metabolic process / interleukin-12-mediated signaling pathway / monosaccharide binding / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / carbohydrate metabolic process / extracellular exosome / nucleus / cytosol / cytoplasm
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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.45 Å
AuthorsSchneider, G. / Thorell, S.
CitationJournal: 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
DepositionMay 14, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 13, 2000Provider: 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: Data collection / Refinement description / Category: diffrn_source / software
Item: _diffrn_source.pdbx_synchrotron_site / _software.classification / _software.name
Revision 1.4Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.5Aug 9, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TRANSALDOLASE
B: TRANSALDOLASE


Theoretical massNumber of molelcules
Total (without water)75,1822
Polymers75,1822
Non-polymers00
Water1,65792
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.570, 113.570, 69.190
Angle α, β, γ (deg.)90.00, 101.37, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is a homodimer constructed from chains A and B

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Components

#1: Protein TRANSALDOLASE /


Mass: 37591.105 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell: MYELOMONOCYTIC LEUKEMIA CELLS / Plasmid: PGEX-2T / Production host: Escherichia coli (E. coli) / References: UniProt: P37837, transaldolase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 92 / 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: 2.33 Å3/Da / Density % sol: 47.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.4
Details: 27% (w/v) PEG 4000, 0.3M ammonium acetate, pH 4.4, VAPOR DIFFUSION, HANGING DROP, temperature 20K
Crystal grow
*PLUS
pH: 7
Details: drop consists of equal volume of protein and reservoir solutions
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
16 mg/mlprotein1drop
250 MTris-HCl1drop
327 %(w/v)PEG40001reservoir
40.08 %1reservoirNaN3
50.3 M1reservoirNH4Ae

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Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 0.995
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 6, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.995 Å / Relative weight: 1
ReflectionResolution: 2.44→23.97 Å / Num. all: 22520 / Num. obs: 22520 / % possible obs: 88.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Biso Wilson estimate: 22.2 Å2 / Rsym value: 0.08 / Net I/σ(I): 7.4
Reflection shellResolution: 2.44→2.57 Å / Redundancy: 2.5 % / Num. unique all: 2951 / Rsym value: 0.206 / % possible all: 79.7
Reflection
*PLUS
Num. measured all: 60447 / Rmerge(I) obs: 0.08
Reflection shell
*PLUS
% possible obs: 79.7 % / Rmerge(I) obs: 0.206 / Mean I/σ(I) obs: 3.3

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Processing

Software
NameVersionClassification
AMoREphasing
CNS1refinement
MAR345data collection
CCP4(SCALA)data scaling
RefinementStarting model: 1ONR, Escherichia coli Transaldolase B

1onr


Resolution: 2.45→19.9 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1001493.25 / 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
Rfree0.258 1141 5.1 %RANDOM
Rwork0.225 ---
all0.254 22371 --
obs0.225 22371 88.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 17.96 Å2 / ksol: 0.339 e/Å3
Displacement parametersBiso mean: 22.1 Å2
Baniso -1Baniso -2Baniso -3
1--0.3 Å20 Å2-5.53 Å2
2--5.97 Å20 Å2
3----5.67 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.28 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 2.45→19.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5046 0 0 92 5138
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
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_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.8
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.491.5
X-RAY DIFFRACTIONc_mcangle_it2.32
X-RAY DIFFRACTIONc_scbond_it2.442
X-RAY DIFFRACTIONc_scangle_it3.392.5
LS refinement shellResolution: 2.45→2.6 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.278 166 4.8 %
Rwork0.244 3276 -
obs--81.7 %
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
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg20.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.8

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