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- PDB-2cwn: Crystal structure of mouse transaldolase -

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Basic information

Entry
Database: PDB / ID: 2cwn
TitleCrystal structure of mouse transaldolase
ComponentsTransaldolase
KeywordsTRANSFERASE / Structural Genomics / Transaldolase / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


Insulin effects increased synthesis of Xylulose-5-Phosphate / Pentose phosphate pathway / glyceraldehyde-3-phosphate metabolic process / transaldolase / transaldolase activity / pentose-phosphate shunt, non-oxidative branch / pentose-phosphate shunt / fructose 6-phosphate metabolic process / monosaccharide binding / carbohydrate binding ...Insulin effects increased synthesis of Xylulose-5-Phosphate / Pentose phosphate pathway / glyceraldehyde-3-phosphate metabolic process / transaldolase / transaldolase activity / pentose-phosphate shunt, non-oxidative branch / pentose-phosphate shunt / fructose 6-phosphate metabolic process / monosaccharide binding / carbohydrate binding / carbohydrate metabolic process / identical protein binding / 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 speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsHanda, N. / Arai, R. / Nishino, A. / Uchikubo, T. / Takemoto, C. / Morita, S. / Kinoshita, Y. / Nagano, Y. / Uda, H. / Terada, T. ...Handa, N. / Arai, R. / Nishino, A. / Uchikubo, T. / Takemoto, C. / Morita, S. / Kinoshita, Y. / Nagano, Y. / Uda, H. / Terada, T. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of mouse transaldolase
Authors: Handa, N. / Arai, R. / Nishino, A. / Uchikubo, T. / Takemoto, C. / Morita, S. / Kinoshita, Y. / Nagano, Y. / Uda, H. / Terada, T. / Shirouzu, M. / Yokoyama, S.
History
DepositionJun 22, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 22, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 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 1.4Oct 25, 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: Transaldolase


Theoretical massNumber of molelcules
Total (without water)72,9892
Polymers72,9892
Non-polymers00
Water6,557364
1
A: Transaldolase


Theoretical massNumber of molelcules
Total (without water)36,4951
Polymers36,4951
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Transaldolase


Theoretical massNumber of molelcules
Total (without water)36,4951
Polymers36,4951
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.050, 108.009, 75.608
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Transaldolase


Mass: 36494.684 Da / Num. of mol.: 2 / Mutation: E210G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Description: cell free protein synthesis / References: UniProt: Q93092, transaldolase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 364 / 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: 2.2 Å3/Da / Density % sol: 44.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.7
Details: Bis-Tris, PEG3350, pH 5.7, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: May 26, 2005 / Details: mirrors
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 38360 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Biso Wilson estimate: 11.8 Å2 / Rsym value: 0.095 / Net I/σ(I): 15.1
Reflection shellResolution: 2.1→2.18 Å / Mean I/σ(I) obs: 3.3 / Rsym value: 0.308 / % possible all: 93.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
MOLREPphasing
CNS1.1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1f05

1f05


Resolution: 2.1→19.98 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2300988.92 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.239 1900 5 %RANDOM
Rwork0.196 ---
obs0.196 38063 99 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 69.7148 Å2 / ksol: 0.400519 e/Å3
Displacement parametersBiso mean: 24.6 Å2
Baniso -1Baniso -2Baniso -3
1-5.8 Å20 Å20 Å2
2--0.03 Å20 Å2
3----5.83 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.18 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 2.1→19.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4921 0 0 364 5285
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d20.6
X-RAY DIFFRACTIONc_improper_angle_d0.74
X-RAY DIFFRACTIONc_mcbond_it1.221.5
X-RAY DIFFRACTIONc_mcangle_it1.862
X-RAY DIFFRACTIONc_scbond_it2.092
X-RAY DIFFRACTIONc_scangle_it3.042.5
Refine LS restraints NCSNCS model details: none
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.262 271 4.5 %
Rwork0.215 5745 -
obs--95.4 %

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