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- PDB-7e78: the structure of cytosolic TaPGI with substrate -

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Basic information

Entry
Database: PDB / ID: 7.0E+78
Titlethe structure of cytosolic TaPGI with substrate
ComponentsGlucose-6-phosphate isomerase
KeywordsISOMERASE / starch / enyzme / dimer / PLANT PROTEIN
Function / homology
Function and homology information


glucose-6-phosphate isomerase / glucose-6-phosphate isomerase activity / glucose 6-phosphate metabolic process / carbohydrate derivative binding / monosaccharide binding / gluconeogenesis / glycolytic process / cytosol
Similarity search - Function
Phosphoglucose isomerase, C-terminal / Phosphoglucose isomerase signature 1. / Phosphoglucose isomerase (PGI) / Phosphoglucose isomerase, conserved site / Phosphoglucose isomerase, SIS domain 1 / Phosphoglucose isomerase, SIS domain 2 / Phosphoglucose isomerase / Phosphoglucose isomerase signature 2. / Glucose-6-phosphate isomerase family profile. / SIS domain superfamily
Similarity search - Domain/homology
6-O-phosphono-alpha-D-glucopyranose / Glucose-6-phosphate isomerase
Similarity search - Component
Biological speciesTriticum aestivum (bread wheat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.21 Å
AuthorsGao, F. / Liu, C.M.
CitationJournal: New Phytol. / Year: 2021
Title: Engineering of the cytosolic form of phosphoglucose isomerase into chloroplasts improves plant photosynthesis and biomass.
Authors: Gao, F. / Zhang, H. / Zhang, W. / Wang, N. / Zhang, S. / Chu, C. / Liu, C.
History
DepositionFeb 25, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 28, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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

Downloads & links

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Assembly

Deposited unit
A: Glucose-6-phosphate isomerase
C: Glucose-6-phosphate isomerase
B: Glucose-6-phosphate isomerase
D: Glucose-6-phosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)249,8366
Polymers249,3164
Non-polymers5202
Water4,179232
1
A: Glucose-6-phosphate isomerase
C: Glucose-6-phosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,1784
Polymers124,6582
Non-polymers5202
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14380 Å2
ΔGint-71 kcal/mol
Surface area36590 Å2
MethodPISA
2
B: Glucose-6-phosphate isomerase
D: Glucose-6-phosphate isomerase


Theoretical massNumber of molelcules
Total (without water)124,6582
Polymers124,6582
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13400 Å2
ΔGint-72 kcal/mol
Surface area37020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)243.616, 74.449, 125.585
Angle α, β, γ (deg.)90.000, 94.119, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein
Glucose-6-phosphate isomerase


Mass: 62328.922 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Triticum aestivum (bread wheat) / Gene: GPI / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q1PBI3, glucose-6-phosphate isomerase
#2: Sugar ChemComp-G6P / 6-O-phosphono-alpha-D-glucopyranose / ALPHA-D-GLUCOSE-6-PHOSPHATE / 6-O-phosphono-alpha-D-glucose / 6-O-phosphono-D-glucose / 6-O-phosphono-glucose


Type: D-saccharide, alpha linking / Mass: 260.136 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13O9P / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
a-D-Glcp6PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 232 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.28 Å3/Da / Density % sol: 46.17 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: MES, PEG MME2000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 3, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.04→36 Å / Num. obs: 112442 / % possible obs: 99.28 % / Redundancy: 3.9 % / Biso Wilson estimate: 42.63 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 7.2
Reflection shellResolution: 2.04→2.08 Å / Num. unique obs: 14 / CC1/2: 0.23

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ujh

3ujh


Resolution: 2.21→35.68 Å / SU ML: 0.3434 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.7594
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2579 1586 1.42 %
Rwork0.2331 110037 -
obs0.2335 111623 99.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 54.53 Å2
Refinement stepCycle: LAST / Resolution: 2.21→35.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17437 0 32 232 17701
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007817878
X-RAY DIFFRACTIONf_angle_d0.949524277
X-RAY DIFFRACTIONf_chiral_restr0.05452753
X-RAY DIFFRACTIONf_plane_restr0.00773111
X-RAY DIFFRACTIONf_dihedral_angle_d13.76856472
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.21-2.280.37111370.40259871X-RAY DIFFRACTION98.13
2.28-2.360.37411460.37099847X-RAY DIFFRACTION98.38
2.36-2.460.37531380.35079875X-RAY DIFFRACTION98.46
2.46-2.570.39771500.32659945X-RAY DIFFRACTION98.79
2.57-2.70.32441450.3119945X-RAY DIFFRACTION99.05
2.7-2.870.35111390.291210004X-RAY DIFFRACTION99.35
2.87-3.10.3171480.277310048X-RAY DIFFRACTION99.72
3.1-3.410.26671470.254910040X-RAY DIFFRACTION99.76
3.41-3.90.26111440.219210089X-RAY DIFFRACTION99.8
3.9-4.910.21521440.178110107X-RAY DIFFRACTION99.43
4.91-35.680.16461480.166110266X-RAY DIFFRACTION99.04

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