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

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Basic information

Entry
Database: PDB / ID: 6nxy
TitleCrystal structure of Arabidopsis thaliana cytosolic triosephosphate isomerase C218D mutant
ComponentsTriosephosphate isomerase, cytosolic
KeywordsISOMERASE / Triosephosphate isomerase Crystal structure mutant dimer redox regulation
Function / homology
Function and homology information


plant-type cell wall / apoplast / plant-type vacuole / plasmodesma / triose-phosphate isomerase / triose-phosphate isomerase activity / chloroplast stroma / response to zinc ion / chloroplast / glycolytic process ...plant-type cell wall / apoplast / plant-type vacuole / plasmodesma / triose-phosphate isomerase / triose-phosphate isomerase activity / chloroplast stroma / response to zinc ion / chloroplast / glycolytic process / gluconeogenesis / 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: 1.05 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 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 1.2Oct 11, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5242
Polymers27,5011
Non-polymers231
Water6,089338
1
A: Triosephosphate isomerase, cytosolic
hetero molecules

A: Triosephosphate isomerase, cytosolic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,0494
Polymers55,0032
Non-polymers462
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455-x-1,y,-z+1/21
Buried area3190 Å2
ΔGint-44 kcal/mol
Surface area19950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.993, 163.486, 97.744
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-681-

HOH

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Components

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


Mass: 27501.264 Da / Num. of mol.: 1 / Mutation: C218D
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 338 / 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: 56.57 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop
Details: 0.2M 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-F / Wavelength: 0.9787 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: 0.9787 Å / Relative weight: 1
ReflectionResolution: 1.05→48.87 Å / Num. obs: 145559 / % possible obs: 100 % / Redundancy: 6 % / Biso Wilson estimate: 6.97 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.035 / Rrim(I) all: 0.086 / Net I/σ(I): 12.8 / Num. measured all: 874388 / Scaling rejects: 1271
Reflection shellResolution: 1.05→1.07 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.496 / Num. unique obs: 7067 / CC1/2: 0.835 / Rpim(I) all: 0.227 / Rrim(I) all: 0.548 / % possible all: 99.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimless0.7.3data scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.24data extraction
xia2data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4OBT

4obt


Resolution: 1.05→40.872 Å / SU ML: 0.07 / Cross valid method: THROUGHOUT / σ(F): 1.49 / Phase error: 14.9
RfactorNum. reflection% reflection
Rfree0.1711 7211 4.96 %
Rwork0.1657 --
obs0.1659 145501 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 37.83 Å2 / Biso mean: 9.63 Å2 / Biso min: 3.07 Å2
Refinement stepCycle: final / Resolution: 1.05→40.872 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1867 0 1 338 2206
Biso mean--8.68 18.89 -
Num. residues----251
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.05-1.06190.21032310.21284543477499
1.0619-1.07440.21662460.200145484794100
1.0744-1.08750.20662360.188945584794100
1.0875-1.10130.20912140.190245524766100
1.1013-1.11580.19462580.180945854843100
1.1158-1.13110.18512270.169845824809100
1.1311-1.14720.17172270.166245954822100
1.1472-1.16440.17872300.164445534783100
1.1644-1.18260.16482380.163746364874100
1.1826-1.2020.17172040.162745694773100
1.202-1.22270.18032160.165946304846100
1.2227-1.24490.17482800.163544904770100
1.2449-1.26890.17262720.164445624834100
1.2689-1.29480.15692680.16145434811100
1.2948-1.32290.16772330.16346004833100
1.3229-1.35370.17612440.16445864830100
1.3537-1.38750.1652490.16545954844100
1.3875-1.42510.17722220.158446044826100
1.4251-1.4670.18022450.154945844829100
1.467-1.51440.15382380.152546024840100
1.5144-1.56850.15252400.14646284868100
1.5685-1.63130.1572440.150346344878100
1.6313-1.70550.16872480.157645834831100
1.7055-1.79540.1622230.160946704893100
1.7954-1.90790.16412460.163546094855100
1.9079-2.05520.1662380.156246754913100
2.0552-2.26210.16562320.158546614893100
2.2621-2.58930.17192490.174346964945100
2.5893-3.26210.18262630.179747174980100
3.2621-40.90250.16022500.164349005150100

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