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- PDB-1d9q: OXIDIZED PEA FRUCTOSE-1,6-BISPHOSPHATASE FORM 1 -

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Basic information

Entry
Database: PDB / ID: 1d9q
TitleOXIDIZED PEA FRUCTOSE-1,6-BISPHOSPHATASE FORM 1
ComponentsFRUCTOSE-1,6-BISPHOSPHATASE
KeywordsHYDROLASE / CHLOROPLAST / PHOTOSYNTHESIS / REDOX REGULATION / THIOREDOXIN / ALLOSTERY / DISULFIDE BRIDGE / CALVIN CYCLE
Function / homology
Function and homology information


sucrose biosynthetic process / fructose-bisphosphatase / reductive pentose-phosphate cycle / fructose 1,6-bisphosphate 1-phosphatase activity / fructose 1,6-bisphosphate metabolic process / fructose metabolic process / fructose 6-phosphate metabolic process / chloroplast stroma / gluconeogenesis / metal ion binding / cytosol
Similarity search - Function
Fructose-1,6-bisphosphatase / Fructose-1,6-bisphosphatase, active site / Fructose-1-6-bisphosphatase active site. / Fructose-1,6-bisphosphatase class 1 / Fructose-1-6-bisphosphatase class I, N-terminal / Fructose-1-6-bisphosphatase class 1, C-terminal / Fructose-1-6-bisphosphatase, N-terminal domain / Fructose-1-6-bisphosphatase, C-terminal domain / D-Maltodextrin-Binding Protein; domain 2 - #80 / Fructose-1,6-Bisphosphatase, subunit A, domain 1 ...Fructose-1,6-bisphosphatase / Fructose-1,6-bisphosphatase, active site / Fructose-1-6-bisphosphatase active site. / Fructose-1,6-bisphosphatase class 1 / Fructose-1-6-bisphosphatase class I, N-terminal / Fructose-1-6-bisphosphatase class 1, C-terminal / Fructose-1-6-bisphosphatase, N-terminal domain / Fructose-1-6-bisphosphatase, C-terminal domain / D-Maltodextrin-Binding Protein; domain 2 - #80 / Fructose-1,6-Bisphosphatase, subunit A, domain 1 / Fructose-1,6-Bisphosphatase; Chain A, domain 1 / D-Maltodextrin-Binding Protein; domain 2 / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Fructose-1,6-bisphosphatase, chloroplastic
Similarity search - Component
Biological speciesPisum sativum (garden pea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsChiadmi, M. / Navaza, A. / Miginiac-Maslow, M. / Jacquot, J.-P. / Cherfils, J.
CitationJournal: EMBO J. / Year: 1999
Title: Redox signalling in the chloroplast: structure of oxidized pea fructose-1,6-bisphosphate phosphatase.
Authors: Chiadmi, M. / Navaza, A. / Miginiac-Maslow, M. / Jacquot, J.P. / Cherfils, J.
History
DepositionOct 29, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 3, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 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
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FRUCTOSE-1,6-BISPHOSPHATASE
B: FRUCTOSE-1,6-BISPHOSPHATASE
C: FRUCTOSE-1,6-BISPHOSPHATASE
D: FRUCTOSE-1,6-BISPHOSPHATASE


Theoretical massNumber of molelcules
Total (without water)156,9684
Polymers156,9684
Non-polymers00
Water6,017334
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12910 Å2
ΔGint-81 kcal/mol
Surface area45540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.940, 113.990, 94.810
Angle α, β, γ (deg.)90.00, 114.38, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
FRUCTOSE-1,6-BISPHOSPHATASE / FBPASE / D-FRUCTOSE-1 / 6-BISPHOSPHATE 1-PHOSPHOHYDROLASE


Mass: 39242.027 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pisum sativum (garden pea) / Organelle: CHLOROPLAST / Production host: Escherichia coli (E. coli) / References: UniProt: P46275, fructose-bisphosphatase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 334 / Source method: isolated from a natural source / Formula: H2O
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: 2.47 Å3/Da / Density % sol: 50.29 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 25% PEG 400, 50MM NA ACETATE (PH 5.5), 50MM MGCL2, 5MM F6P, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
125 %PEG4001reservoir
250 mMsodium acetate1reservoir
350 mM1reservoirMgCl2
45 mMF6P1reservoir

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.965
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.965 Å / Relative weight: 1
ReflectionResolution: 2.4→10 Å / Num. all: 53059 / Num. obs: 52402 / % possible obs: 89 % / Observed criterion σ(F): 2 / Redundancy: 2.7 % / Biso Wilson estimate: 39.5 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 15.7
Reflection shellResolution: 2.4→2.42 Å / Num. unique all: 1228 / % possible all: 84
Reflection
*PLUS
Num. measured all: 242800
Reflection shell
*PLUS
% possible obs: 84 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLOR3.851refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1SPI

1spi


Resolution: 2.4→10 Å / σ(F): 2
RfactorNum. reflection
Rfree0.236 5273
Rwork0.186 -
all-52402
obs-52266
Refinement stepCycle: LAST / Resolution: 2.4→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9850 0 0 334 10184
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_angle_d1.36
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_deg1.36

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