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- PDB-6cg9: Crystal structure of Triosephosphate Isomerase from Zea mays (mex... -

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Basic information

Entry
Database: PDB / ID: 6cg9
TitleCrystal structure of Triosephosphate Isomerase from Zea mays (mexican corn)
ComponentsTriosephosphate isomerase, cytosolic
KeywordsISOMERASE / Glycolysis / TIM-barrel
Function / homology
Function and homology information


glyceraldehyde-3-phosphate biosynthetic process / glycerol catabolic process / triose-phosphate isomerase / triose-phosphate isomerase activity / gluconeogenesis / glycolytic process / cytosol
Similarity search - Function
Triosephosphate isomerase, bacterial/eukaryotic / Triosephosphate isomerase, active site / Triosephosphate isomerase active site. / Triosephosphate isomerase / Triosephosphate isomerase superfamily / Triosephosphate isomerase / Triosephosphate isomerase (TIM) family profile. / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel ...Triosephosphate isomerase, bacterial/eukaryotic / Triosephosphate isomerase, active site / Triosephosphate isomerase active site. / Triosephosphate isomerase / Triosephosphate isomerase superfamily / Triosephosphate isomerase / Triosephosphate isomerase (TIM) family profile. / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Triosephosphate isomerase, cytosolic
Similarity search - Component
Biological speciesZea mays (maize)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsRomero-Romero, S. / Fernandez-Velasco, D.A. / Rodriguez-Romero, A.
Funding support Mexico, 4items
OrganizationGrant numberCountry
Consejo Nacional de Ciencia y Tecnologia (CONACYT)254514 Mexico
PAPIIT, DGAPA, UNAMIN220516 Mexico
Consejo Nacional de Ciencia y Tecnologia (CONACYT)221169 Mexico
PAPIIT, DGAPA, UNAMIN207613 Mexico
CitationJournal: Arch. Biochem. Biophys. / Year: 2018
Title: Structure and conformational stability of the triosephosphate isomerase from Zea mays. Comparison with the chemical unfolding pathways of other eukaryotic TIMs.
Authors: Romero-Romero, S. / Becerril-Sesin, L.A. / Costas, M. / Rodriguez-Romero, A. / Fernandez-Velasco, D.A.
History
DepositionFeb 19, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 10, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 17, 2018Group: Data collection / Database references / Structure summary
Category: citation / entity
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _entity.formula_weight
Revision 1.2Jan 15, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 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: Triosephosphate isomerase, cytosolic
B: Triosephosphate isomerase, cytosolic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,8194
Polymers54,6682
Non-polymers1512
Water11,061614
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3450 Å2
ΔGint-27 kcal/mol
Surface area19780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.430, 49.400, 74.600
Angle α, β, γ (deg.)90.00, 92.23, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Triosephosphate isomerase, cytosolic / / Triose-phosphate isomerase


Mass: 27334.107 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zea mays (maize) / Plasmid: pET28b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P12863, triose-phosphate isomerase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 614 / 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: 2.31 Å3/Da / Density % sol: 46.72 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2 M Magnesium acetate tetrahydrate, 0.1 M Sodium cacadylate trihydrate pH: 6.5, 20% w/v Polyethylene glicol 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 18, 2014 / Details: Mirrors
RadiationMonochromator: VariMax HF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→30.63 Å / Num. obs: 46447 / % possible obs: 99.92 % / Redundancy: 2 % / Biso Wilson estimate: 19.2 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.046 / Rrim(I) all: 0.065 / Net I/σ(I): 8.84
Reflection shellResolution: 1.8→1.864 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 3.08 / Num. unique obs: 4594 / CC1/2: 0.903 / Rpim(I) all: 0.2 / Rrim(I) all: 0.282 / % possible all: 99.54

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2JK2

2jk2


Resolution: 1.8→30.628 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.31
RfactorNum. reflection% reflection
Rfree0.1881 2306 4.97 %
Rwork0.1455 --
obs0.1476 46424 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.8→30.628 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3785 0 10 618 4413
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073868
X-RAY DIFFRACTIONf_angle_d0.9795261
X-RAY DIFFRACTIONf_dihedral_angle_d13.0921377
X-RAY DIFFRACTIONf_chiral_restr0.04608
X-RAY DIFFRACTIONf_plane_restr0.006679
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.83910.21031520.16382728X-RAY DIFFRACTION100
1.8391-1.88190.21181230.17482732X-RAY DIFFRACTION100
1.8819-1.9290.23681270.16932737X-RAY DIFFRACTION100
1.929-1.98110.1841590.15192718X-RAY DIFFRACTION100
1.9811-2.03940.19331440.14932736X-RAY DIFFRACTION100
2.0394-2.10520.20311610.14892737X-RAY DIFFRACTION100
2.1052-2.18040.20641350.14682749X-RAY DIFFRACTION100
2.1804-2.26770.19751610.14782740X-RAY DIFFRACTION100
2.2677-2.37090.20681830.15362717X-RAY DIFFRACTION100
2.3709-2.49580.19061390.15092751X-RAY DIFFRACTION100
2.4958-2.65210.21461220.14682769X-RAY DIFFRACTION100
2.6521-2.85680.18771690.15332747X-RAY DIFFRACTION100
2.8568-3.1440.20211310.15232766X-RAY DIFFRACTION100
3.144-3.59830.17211130.13222819X-RAY DIFFRACTION100
3.5983-4.53110.14161220.12772820X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 66.99 Å / Origin y: -0.8054 Å / Origin z: 92.853 Å
111213212223313233
T0.105 Å20.0196 Å20.0086 Å2-0.081 Å20.0014 Å2--0.0881 Å2
L0.588 °20.1346 °20.1847 °2-0.2105 °20.1204 °2--0.3812 °2
S0.0012 Å °0.0599 Å °-0.0018 Å °-0.0191 Å °0.0049 Å °-0.0036 Å °-0.0641 Å °0.0106 Å °-0.0001 Å °
Refinement TLS groupSelection details: all

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