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- PDB-9led: Rice FBA1 in complex with fructose bisphosphate -

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Basic information

Entry
Database: PDB / ID: 9led
TitleRice FBA1 in complex with fructose bisphosphate
ComponentsFructose-bisphosphate aldolase 1, cytoplasmic
KeywordsHYDROLASE / fructose bisphosphate aldolase
Function / homology
Function and homology information


root development / fructose-bisphosphate aldolase / fructose-bisphosphate aldolase activity / fructose 1,6-bisphosphate metabolic process / glycolytic process / gluconeogenesis / cytosol / cytoplasm
Similarity search - Function
Fructose-bisphosphate aldolase class-I active site / Fructose-bisphosphate aldolase class-I active site. / Fructose-bisphosphate aldolase, class-I / Fructose-bisphosphate aldolase class-I / Aldolase-type TIM barrel
Similarity search - Domain/homology
1,6-di-O-phosphono-D-fructose / Fructose-bisphosphate aldolase 1, cytoplasmic
Similarity search - Component
Biological speciesOryza sativa Japonica Group (Japanese rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsGao, A.M. / Zhou, C.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Rice FBA1 in complex with fructose bisphosphate
Authors: Gao, A.M. / Zhou, C.
History
DepositionJan 7, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jan 14, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fructose-bisphosphate aldolase 1, cytoplasmic
B: Fructose-bisphosphate aldolase 1, cytoplasmic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,6034
Polymers73,9222
Non-polymers6802
Water4,972276
1
A: Fructose-bisphosphate aldolase 1, cytoplasmic
hetero molecules

A: Fructose-bisphosphate aldolase 1, cytoplasmic
hetero molecules

B: Fructose-bisphosphate aldolase 1, cytoplasmic
hetero molecules

B: Fructose-bisphosphate aldolase 1, cytoplasmic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,2058
Polymers147,8454
Non-polymers1,3604
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
crystal symmetry operation1_655x+1,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area7790 Å2
ΔGint-21 kcal/mol
Surface area47370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.137, 102.384, 92.980
Angle α, β, γ (deg.)90.00, 93.11, 90.00
Int Tables number5
Space group name H-MI121
Components on special symmetry positions
IDModelComponents
11A-633-

HOH

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Components

#1: Protein Fructose-bisphosphate aldolase 1, cytoplasmic / Cytoplasmic aldolase / cALD / Gravity-specific protein GSC 233


Mass: 36961.230 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa Japonica Group (Japanese rice)
Gene: FBA1, FBA, Os05g0402700, LOC_Os05g33380, OSJNBa0035J16.18, OSJNBb0006J12.6
Production host: Escherichia coli (E. coli) / References: UniProt: P17784, fructose-bisphosphate aldolase
#2: Chemical ChemComp-P6F / 1,6-di-O-phosphono-D-fructose


Mass: 340.116 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O12P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 276 / 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: 2.26 Å3/Da / Density % sol: 45.67 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97861 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 22, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97861 Å / Relative weight: 1
ReflectionResolution: 2.2→46.42 Å / Num. obs: 64329 / % possible obs: 92.77 % / Redundancy: 6.5 % / CC1/2: 1 / Rmerge(I) obs: 0.039 / Rpim(I) all: 0.01652 / Net I/σ(I): 30.2
Reflection shellResolution: 2.2→2.23 Å / Rmerge(I) obs: 0.4869 / Num. unique obs: 1788 / CC1/2: 0.831 / Rpim(I) all: 0.2419

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Processing

Software
NameVersionClassification
PHENIX(1.21.2_5419: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→46.42 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2073 3133 4.87 %
Rwork0.19 --
obs0.1908 64329 92.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→46.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5193 0 0 276 5469
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055281
X-RAY DIFFRACTIONf_angle_d0.7577153
X-RAY DIFFRACTIONf_dihedral_angle_d17.0831963
X-RAY DIFFRACTIONf_chiral_restr0.051820
X-RAY DIFFRACTIONf_plane_restr0.004916
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.230.33861020.29171778X-RAY DIFFRACTION60
2.23-2.270.32171130.29051904X-RAY DIFFRACTION62
2.27-2.310.2494980.2662066X-RAY DIFFRACTION71
2.31-2.350.3061150.26172377X-RAY DIFFRACTION79
2.35-2.40.28251460.24782548X-RAY DIFFRACTION85
2.4-2.450.24781440.24042861X-RAY DIFFRACTION97
2.45-2.50.28561720.25122999X-RAY DIFFRACTION99
2.5-2.560.23521820.22842978X-RAY DIFFRACTION100
2.56-2.620.23241610.23522946X-RAY DIFFRACTION100
2.62-2.690.28781610.22382939X-RAY DIFFRACTION99
2.69-2.770.2881550.22613018X-RAY DIFFRACTION100
2.77-2.860.18681200.22333047X-RAY DIFFRACTION99
2.86-2.960.2771330.21142997X-RAY DIFFRACTION100
2.96-3.080.24871220.21613024X-RAY DIFFRACTION100
3.08-3.220.22651490.21323006X-RAY DIFFRACTION100
3.22-3.390.2571310.21172952X-RAY DIFFRACTION100
3.39-3.60.2061140.19712977X-RAY DIFFRACTION98
3.6-3.880.15841680.17222952X-RAY DIFFRACTION99
3.88-4.270.18341580.15522969X-RAY DIFFRACTION99
4.27-4.890.15711910.14482921X-RAY DIFFRACTION98
4.89-6.160.21431430.16432982X-RAY DIFFRACTION99
6.16-46.420.12581550.14092955X-RAY DIFFRACTION98

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