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- PDB-9qm7: Crystal structure of S-nitrosylated triose phosphate isomerase fr... -

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Basic information

Entry
Database: PDB / ID: 9qm7
TitleCrystal structure of S-nitrosylated triose phosphate isomerase from Chlamydomonas reinhardtii
ComponentsChloroplast triosephosphate isomerase
KeywordsISOMERASE / TIM-barrel fold / S-nitrosylation / chloroplast
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
Chloroplast triosephosphate isomerase
Similarity search - Component
Biological speciesChlamydomonas reinhardtii (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsFanti, S. / Fermani, 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
DepositionMar 21, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5944
Polymers27,1201
Non-polymers4753
Water6,233346
1
A: Chloroplast triosephosphate isomerase
hetero molecules

A: Chloroplast triosephosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,1898
Polymers54,2392
Non-polymers9496
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4_555x,-y,-z1
MethodPISA
Unit cell
Length a, b, c (Å)59.893, 93.361, 100.499
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-632-

HOH

21A-693-

HOH

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Components

#1: Protein Chloroplast triosephosphate isomerase


Mass: 27119.727 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: S-nitrosylated cysteine 14 / Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Gene: TIM, CHLRE_01g029300v5 / Organ: chloroplast / Production host: Escherichia coli (E. coli) / References: UniProt: Q5S7Y5
#2: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 346 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.34 Å3/Da / Density % sol: 47.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 50%-55% v/v MPD, 0.1 M Hepes-NaOH (pH 7.5)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 6, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.2→35.59 Å / Num. obs: 88037 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 12.1 % / Biso Wilson estimate: 11.5 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.044 / Rpim(I) all: 0.014 / Rrim(I) all: 0.046 / Χ2: 0.75 / Net I/σ(I): 42.2
Reflection shellResolution: 1.2→1.22 Å / Redundancy: 13 % / Rmerge(I) obs: 0.123 / Mean I/σ(I) obs: 15.7 / Num. unique obs: 4311 / CC1/2: 0.995 / Rpim(I) all: 0.036 / Rrim(I) all: 0.128 / Χ2: 0.47 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.19rc7_4070: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.2→35.59 Å / SU ML: 0.09 / Cross valid method: FREE R-VALUE / σ(F): 0.46 / Phase error: 15.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1691 8481 4.98 %random selection
Rwork0.1579 ---
obs0.1585 87994 99.99 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17 Å2
Refinement stepCycle: LAST / Resolution: 1.2→35.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1892 0 31 346 2269
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0152074
X-RAY DIFFRACTIONf_angle_d1.4742837
X-RAY DIFFRACTIONf_dihedral_angle_d13.861311
X-RAY DIFFRACTIONf_chiral_restr0.096315
X-RAY DIFFRACTIONf_plane_restr0.013367
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2-1.210.17722850.18045374X-RAY DIFFRACTION100
1.21-1.230.23012700.17635411X-RAY DIFFRACTION100
1.23-1.240.17473070.17325375X-RAY DIFFRACTION100
1.24-1.260.23633150.18085380X-RAY DIFFRACTION100
1.26-1.280.18863060.17625381X-RAY DIFFRACTION100
1.28-1.290.18843120.17335363X-RAY DIFFRACTION100
1.29-1.310.20173350.17895330X-RAY DIFFRACTION100
1.31-1.330.18362610.17665415X-RAY DIFFRACTION100
1.33-1.350.17062530.17025448X-RAY DIFFRACTION100
1.35-1.370.19072710.17345333X-RAY DIFFRACTION100
1.37-1.40.1692620.16925456X-RAY DIFFRACTION100
1.4-1.420.18293130.16815404X-RAY DIFFRACTION100
1.42-1.450.18012430.16455372X-RAY DIFFRACTION100
1.45-1.480.20052820.1555408X-RAY DIFFRACTION100
1.48-1.510.19232570.15525414X-RAY DIFFRACTION100
1.51-1.550.15362790.15045397X-RAY DIFFRACTION100
1.55-1.590.15752640.15255459X-RAY DIFFRACTION100
1.59-1.630.16452620.15375378X-RAY DIFFRACTION100
1.63-1.680.16273030.15495357X-RAY DIFFRACTION100
1.68-1.730.15532960.155385X-RAY DIFFRACTION100
1.73-1.790.18822600.15325440X-RAY DIFFRACTION100
1.79-1.860.14522840.14915375X-RAY DIFFRACTION100
1.86-1.950.14432480.15025435X-RAY DIFFRACTION100
1.95-2.050.1632920.15235409X-RAY DIFFRACTION100
2.05-2.180.142750.14225338X-RAY DIFFRACTION100
2.18-2.350.16512900.14965402X-RAY DIFFRACTION100
2.35-2.580.15933050.15215390X-RAY DIFFRACTION100
2.59-2.960.1672950.1525379X-RAY DIFFRACTION100
2.96-3.730.14812730.14315439X-RAY DIFFRACTION100
3.73-35.590.20352830.1855378X-RAY DIFFRACTION100

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