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

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Basic information

Entry
Database: PDB / ID: 6nxr
TitleCrystal structure of Arabidopsis thaliana cytosolic triosephosphate isomerase C13D mutant
ComponentsTriosephosphate isomerase, cytosolic
KeywordsISOMERASE / Triosephosphate isomerase Crystal structure mutant dimer redox regulation
Function / homology
Function and homology information


plant-type cell wall / plasmodesma / apoplast / plant-type vacuole / triose-phosphate isomerase / triose-phosphate isomerase activity / chloroplast stroma / response to zinc ion / chloroplast / gluconeogenesis ...plant-type cell wall / plasmodesma / apoplast / 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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.3 Å
AuthorsJimenez-Sandoval, P. / Diaz-Quezada, C. / Torres-Larios, A. / Brieba, L.G.
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 9, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6163
Polymers27,5011
Non-polymers1152
Water6,161342
1
A: Triosephosphate isomerase, cytosolic
hetero molecules

A: Triosephosphate isomerase, cytosolic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,2336
Polymers55,0032
Non-polymers2304
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455-x-1,y,-z+1/21
Buried area3520 Å2
ΔGint-34 kcal/mol
Surface area19390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.682, 163.850, 98.093
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-637-

HOH

21A-690-

HOH

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Components

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


Mass: 27501.264 Da / Num. of mol.: 1 / Mutation: C13D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: CTIMC, At3g55440, T22E16.100 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P48491, triose-phosphate isomerase
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: 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
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 342 / 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: 2.83 Å3/Da / Density % sol: 56.47 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Sodium acetate trihydrate 0.1M 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-G / Wavelength: 0.9786 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 26, 2017
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.3→42.08 Å / Num. obs: 76329 / % possible obs: 99.1 % / Redundancy: 5.5 % / CC1/2: 0.996 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.032 / Rrim(I) all: 0.076 / Net I/σ(I): 12
Reflection shellResolution: 1.3→1.32 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.435 / Num. unique obs: 3682 / CC1/2: 0.921 / Rpim(I) all: 0.2 / Rrim(I) all: 0.48 / % possible all: 97.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimless0.7.3data scaling
PHASERphasing
REFMAC5.8.0238refinement
PDB_EXTRACT3.24data extraction
xia2data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→41 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.968 / SU B: 1.239 / SU ML: 0.023 / SU R Cruickshank DPI: 0.0365 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.037 / ESU R Free: 0.036
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1538 3839 5 %RANDOM
Rwork0.1306 ---
obs0.1318 72474 98.95 %-
Solvent computationIon probe radii: 1 Å / Shrinkage radii: 1 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 59.22 Å2 / Biso mean: 14.438 Å2 / Biso min: 7.29 Å2
Baniso -1Baniso -2Baniso -3
1-0.62 Å2-0 Å20 Å2
2---1.06 Å2-0 Å2
3---0.44 Å2
Refinement stepCycle: final / Resolution: 1.3→41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1846 0 7 342 2195
Biso mean--20.46 30.88 -
Num. residues----248
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0132002
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171874
X-RAY DIFFRACTIONr_angle_refined_deg1.5911.6232742
X-RAY DIFFRACTIONr_angle_other_deg1.5911.5784341
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.215273
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.98823.66790
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.93315321
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.318159
X-RAY DIFFRACTIONr_chiral_restr0.0840.2263
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022344
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02411
X-RAY DIFFRACTIONr_rigid_bond_restr1.89333875
X-RAY DIFFRACTIONr_sphericity_free24.2845229
X-RAY DIFFRACTIONr_sphericity_bonded10.56153944
LS refinement shellResolution: 1.3→1.334 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.208 285 -
Rwork0.184 5247 -
all-5532 -
obs--97.58 %

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