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- PDB-6nxw: Crystal structure of Arabidopsis thaliana cytosolic triosephospha... -

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Basic information

Entry
Database: PDB / ID: 6nxw
TitleCrystal structure of Arabidopsis thaliana cytosolic triosephosphate isomerase C218S mutant
ComponentsTriosephosphate isomerase, cytosolic
KeywordsISOMERASE / Triosephosphate isomerase Crystal structure mutant dimer redox regulation
Function / homology
Function and homology information


plant-type cell wall / apoplast / plasmodesma / plant-type vacuole / triose-phosphate isomerase / triose-phosphate isomerase activity / chloroplast stroma / response to zinc ion / chloroplast / gluconeogenesis ...plant-type cell wall / apoplast / plasmodesma / plant-type vacuole / triose-phosphate isomerase / triose-phosphate isomerase activity / chloroplast stroma / response to zinc ion / chloroplast / gluconeogenesis / glycolytic process / copper ion binding / mitochondrion / plasma membrane / 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
Triosephosphate isomerase, cytosolic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.95 Å
AuthorsJimenez-Sandoval, P. / Diaz-Quezada, C. / Torres-Larios, A. / Brieba, L.G.
Funding support Mexico, 1items
OrganizationGrant numberCountry
Consejo Nacional de Ciencia y Tecnologia (CONACYT)Fronteras de la Ciencia 11 Mexico
CitationJournal: Plant J. / Year: 2019
Title: Structural basis for the modulation of plant cytosolic triosephosphate isomerase activity by mimicry of redox-based modifications.
Authors: Castro-Torres, E. / Jimenez-Sandoval, P. / Romero-Romero, S. / Fuentes-Pascacio, A. / Lopez-Castillo, L.M. / Diaz-Quezada, C. / Fernandez-Velasco, D.A. / Torres-Larios, A. / Brieba, L.G.
History
DepositionFeb 10, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 19, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 2, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
C: Triosephosphate isomerase, cytosolic
D: Triosephosphate isomerase, cytosolic


Theoretical massNumber of molelcules
Total (without water)109,8934
Polymers109,8934
Non-polymers00
Water10,124562
1
A: Triosephosphate isomerase, cytosolic

C: Triosephosphate isomerase, cytosolic


Theoretical massNumber of molelcules
Total (without water)54,9472
Polymers54,9472
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_445y-1,-x+y-1,z+1/61
Buried area2950 Å2
ΔGint-26 kcal/mol
Surface area18950 Å2
MethodPISA
2
B: Triosephosphate isomerase, cytosolic
D: Triosephosphate isomerase, cytosolic


Theoretical massNumber of molelcules
Total (without water)54,9472
Polymers54,9472
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2940 Å2
ΔGint-26 kcal/mol
Surface area18440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.351, 94.351, 204.218
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

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


Mass: 27473.254 Da / Num. of mol.: 4 / Mutation: C218S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: CTIMC, At3g55440, T22E16.100 / Production host: Escherichia coli (E. coli) / References: UniProt: P48491, triose-phosphate isomerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 562 / 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: 2.39 Å3/Da / Density % sol: 48.49 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Magnesium chloride hexahydrate 0.1 M TRIS hydrochloride 8.5 30 % w/v Polyethylene glycol 4,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9787 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jun 26, 2017
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 1.95→75.98 Å / Num. obs: 74675 / % possible obs: 99.9 % / Redundancy: 5.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.021 / Rrim(I) all: 0.052 / Net I/σ(I): 21.2
Reflection shellResolution: 1.95→1.99 Å / Redundancy: 4 % / Rmerge(I) obs: 0.169 / Num. unique obs: 4584 / CC1/2: 0.952 / Rpim(I) all: 0.095 / Rrim(I) all: 0.194 / % possible all: 99.3

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Processing

Software
NameVersionClassification
Aimless0.7.2data scaling
REFMAC5.8.0238refinement
PDB_EXTRACT3.24data extraction
xia2data reduction
PHASERphasing
RefinementResolution: 1.95→75.98 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.948 / SU B: 2.645 / SU ML: 0.076 / SU R Cruickshank DPI: 0.1439 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.144 / ESU R Free: 0.12
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1803 3805 5.1 %RANDOM
Rwork0.1595 ---
obs0.1606 70788 99.86 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å
Displacement parametersBiso max: 65.74 Å2 / Biso mean: 18.833 Å2 / Biso min: 8.65 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å2-0.03 Å2-0 Å2
2---0.06 Å20 Å2
3---0.2 Å2
Refinement stepCycle: final / Resolution: 1.95→75.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7393 0 0 562 7955
Biso mean---25.35 -
Num. residues----996
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0137587
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177068
X-RAY DIFFRACTIONr_angle_refined_deg1.2791.62210342
X-RAY DIFFRACTIONr_angle_other_deg1.321.57116321
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.10951005
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.07923.709337
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.738151188
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.331532
X-RAY DIFFRACTIONr_chiral_restr0.0590.21009
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.028683
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021537
LS refinement shellResolution: 1.95→2.001 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.226 292 -
Rwork0.177 5166 -
all-5458 -
obs--98.98 %

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