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- PDB-9r6m: Crystal structure of C14S mutant of triosephosphate isomerase fro... -

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Basic information

Entry
Database: PDB / ID: 9r6m
TitleCrystal structure of C14S mutant of triosephosphate isomerase from Chamydomonas reinhardtii
ComponentsChloroplast triosephosphate isomerase
KeywordsISOMERASE / TIM-BARREL FOLD / CHLOROPLAST / MUTANT
Function / homology
Function and homology information


triose-phosphate isomerase activity / glyceraldehyde-3-phosphate biosynthetic process / glycerol catabolic process / glycolytic process / gluconeogenesis / 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-type TIM barrel
Similarity search - Domain/homology
PHOSPHATE ION / Chloroplast triosephosphate isomerase
Similarity search - Component
Biological speciesChlamydomonas reinhardtii (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.55 Å
AuthorsFermani, S. / Fanti, S. / Gabellini, G. / Zaffagnini, M. / Meloni, M. / Peppi, G.M.E.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Plant Sci. / Year: 2025
Title: Molecular and structural basis for nitrosoglutathione-dependent redox regulation of triosephosphate isomerase from Chlamydomonas reinhardtii.
Authors: Meloni, M. / Mattioli, E.J. / Fanti, S. / Peppi, G.M.E. / Bin, T. / Gabellini, G. / Tedesco, D. / Henri, J. / Trost, P. / Lemaire, S.D. / Calvaresi, M. / Fermani, S. / Zaffagnini, M.
History
DepositionMay 13, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 1, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chloroplast triosephosphate isomerase
B: Chloroplast triosephosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,4345
Polymers54,1492
Non-polymers2853
Water1086
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3960 Å2
ΔGint-39 kcal/mol
Surface area18710 Å2
Unit cell
Length a, b, c (Å)98.975, 99.478, 102.376
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Chloroplast triosephosphate isomerase


Mass: 27074.664 Da / Num. of mol.: 2 / Mutation: C14S
Source method: isolated from a genetically manipulated source
Details: Mutant C14S / Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Cell: chloroplast / Gene: TIM, CHLRE_01g029300v5 / Plasmid: pET-3c-His/BL21 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5S7Y5
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 4.2 Å3/Da / Density % sol: 70.7 % / Description: needle like
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 0.1 M Bis-Tris (pH 5.0) and 17.5% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: May 1, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 3.55→98.97 Å / Num. obs: 12570 / % possible obs: 99 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 3 / Redundancy: 6.4 % / CC1/2: 0.972 / Rmerge(I) obs: 0.445 / Rpim(I) all: 0.19 / Rrim(I) all: 0.485 / Χ2: 1.01 / Net I/σ(I): 4.3
Reflection shellResolution: 3.55→3.89 Å / Redundancy: 5.9 % / Rmerge(I) obs: 1.565 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 2873 / CC1/2: 0.521 / Rpim(I) all: 0.686 / Rrim(I) all: 1.715 / Χ2: 1.05

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Processing

Software
NameVersionClassification
PHENIX(1.19rc7_4070: ???)refinement
SCALAdata scaling
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.55→21.65 Å / SU ML: 0.6 / Cross valid method: FREE R-VALUE / σ(F): 0.03 / Phase error: 34.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2985 1240 5.35 %
Rwork0.279 --
obs0.28 12459 98.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 53.71 Å2
Refinement stepCycle: LAST / Resolution: 3.55→21.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3786 0 15 6 3807
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033872
X-RAY DIFFRACTIONf_angle_d0.5825258
X-RAY DIFFRACTIONf_dihedral_angle_d6.31533
X-RAY DIFFRACTIONf_chiral_restr0.042591
X-RAY DIFFRACTIONf_plane_restr0.004681
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.55-3.690.39991350.37822398X-RAY DIFFRACTION98
3.69-3.860.36391140.31562441X-RAY DIFFRACTION98
3.86-4.060.32381980.29232286X-RAY DIFFRACTION95
4.06-4.310.27171350.25552460X-RAY DIFFRACTION99
4.31-4.640.20531480.22462451X-RAY DIFFRACTION100
4.64-5.110.23071000.22232515X-RAY DIFFRACTION100
5.11-5.830.28461520.25652465X-RAY DIFFRACTION100
5.83-7.30.27441370.26272457X-RAY DIFFRACTION100
7.3-21.650.34381210.31742470X-RAY DIFFRACTION99

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