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- PDB-7e77: The structure of cytosolic TaPGI -

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Basic information

Entry
Database: PDB / ID: 7.0E+77
TitleThe structure of cytosolic TaPGI
ComponentsGlucose-6-phosphate isomerase
KeywordsISOMERASE / starch / BIOSYNTHETIC PROTEIN
Function / homology
Function and homology information


glucose-6-phosphate isomerase / glucose-6-phosphate isomerase activity / carbohydrate derivative binding / gluconeogenesis / glycolytic process
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
Glucose-6-phosphate isomerase
Similarity search - Component
Biological speciesTriticum aestivum (bread wheat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04 Å
AuthorsGao, F. / Liu, C.M.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)32070280 China
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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)249,3164
Polymers249,3164
Non-polymers00
Water10,413578
1
A: Glucose-6-phosphate isomerase
C: 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 area13360 Å2
ΔGint-71 kcal/mol
Surface area37290 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 area12350 Å2
ΔGint-70 kcal/mol
Surface area36020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)244.317, 74.902, 125.338
Angle α, β, γ (deg.)90.000, 93.797, 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 578 / 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: 2.3 Å3/Da / Density % sol: 46.61 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2 M NaCl, 0.1 M Bis-Tris pH 5.5, 25% (w/v) Polyethylene glycol 3350

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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: Apr 7, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 132222 / % possible obs: 99.69 % / Redundancy: 5.2 % / Biso Wilson estimate: 33.08 Å2 / Rpim(I) all: 0.045 / Net I/σ(I): 23.9
Reflection shellResolution: 2→2.03 Å / Num. unique obs: 20 / CC1/2: 0.357

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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: 2.04→37.91 Å / SU ML: 0.271 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.2462
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2598 2004 1.53 %
Rwork0.2541 128990 -
obs0.2542 130994 91.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 59.88 Å2
Refinement stepCycle: LAST / Resolution: 2.04→37.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17252 0 0 578 17830
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002117652
X-RAY DIFFRACTIONf_angle_d0.524323952
X-RAY DIFFRACTIONf_chiral_restr0.04162708
X-RAY DIFFRACTIONf_plane_restr0.00373074
X-RAY DIFFRACTIONf_dihedral_angle_d12.42526398
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.04-2.10.36341480.37058849X-RAY DIFFRACTION88.06
2.1-2.150.3331430.33979642X-RAY DIFFRACTION96.42
2.15-2.220.31111470.32799631X-RAY DIFFRACTION96.13
2.22-2.290.29631460.31829536X-RAY DIFFRACTION95.36
2.29-2.370.33011440.30879560X-RAY DIFFRACTION95.17
2.37-2.460.33051460.29469463X-RAY DIFFRACTION94.84
2.46-2.580.281530.29019485X-RAY DIFFRACTION94.17
2.58-2.710.29141460.27819406X-RAY DIFFRACTION93.56
2.71-2.880.25871510.27519330X-RAY DIFFRACTION93.17
2.88-3.10.2751440.26069403X-RAY DIFFRACTION93.31
3.1-3.420.25821430.24639394X-RAY DIFFRACTION93.29
3.42-3.910.23241380.22828967X-RAY DIFFRACTION88.59
3.91-4.920.22121170.21487760X-RAY DIFFRACTION76.5
4.92-37.910.21071380.20258564X-RAY DIFFRACTION82.73

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