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- PDB-1spi: CRYSTAL STRUCTURE OF SPINACH CHLOROPLAST FRUCTOSE-1,6-BISPHOSPHAT... -

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Basic information

Entry
Database: PDB / ID: 1spi
TitleCRYSTAL STRUCTURE OF SPINACH CHLOROPLAST FRUCTOSE-1,6-BISPHOSPHATASE AT 2.8 ANGSTROMS RESOLUTION
ComponentsFRUCTOSE 1,6-BISPHOSPHATASE
KeywordsHYDROLASE (PHOSPHORIC MONOESTER)
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 / gluconeogenesis / metal ion binding ...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 / gluconeogenesis / metal ion binding / cytoplasm / 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 speciesSpinacia oleracea (spinach)
MethodX-RAY DIFFRACTION / Resolution: 2.8 Å
AuthorsVilleret, V. / Huang, S. / Zhang, Y. / Xue, Y. / Lipscomb, W.N.
Citation
Journal: Biochemistry / Year: 1995
Title: Crystal structure of spinach chloroplast fructose-1,6-bisphosphatase at 2.8 A resolution.
Authors: Villeret, V. / Huang, S. / Zhang, Y. / Xue, Y. / Lipscomb, W.N.
#1: Journal: J.Mol.Biol. / Year: 1994
Title: Toward a Mechanism for the Allosteric Transition of Pig Kidney Fructose-1,6-Bisphosphatase
Authors: Zhang, Y. / Liang, J.-Y. / Huang, S. / Lipscomb, W.N.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1994
Title: Crystal Structure of Fructose-1,6-Bisphosphatase Complexed with Fructose 2,6-Bisphosphate, AMP and Zn2+ at 2.0 Angstroms Resolution. Aspects of Synergism between Inhibitors
Authors: Xue, Y. / Huang, S. / Liang, J.-Y. / Zhang, Y. / Lipscomb, W.N.
#3: Journal: Biochemistry / Year: 1993
Title: Crystallographic Studies of the Catalytic Mechanism of the Neutral Form of Fructose-1,6-Bisphosphatase
Authors: Zhang, Y. / Liang, J.-Y. / Huang, S. / Ke, H. / Lipscomb, W.N.
History
DepositionDec 14, 1994Processing site: BNL
Revision 1.0Feb 27, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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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)156,7254
Polymers156,7254
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12820 Å2
ΔGint-70 kcal/mol
Surface area56010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.100, 85.700, 105.800
Angle α, β, γ (deg.)90.00, 103.10, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
FRUCTOSE 1,6-BISPHOSPHATASE


Mass: 39181.125 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Spinacia oleracea (spinach) / References: UniProt: P22418, fructose-bisphosphatase

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.14 Å3/Da / Density % sol: 42.61 %
Crystal growDetails: COMPND PH 5.2.
Crystal grow
*PLUS
pH: 5.2 / Method: microdialysis
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110-15 mg/mlenzyme11
280 mM12NaAc
30.3 mMammonium sulfate12
40.3 mMNa citrate12
52 %(w/v)PEG145012
62 %(w/v)PEG335012
74 mM12NaN3
80.2 mMEDTA12
90.3 mMoctylphenoxypoly(ethoxyethanol)12

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Data collection

ReflectionNum. obs: 29281 / % possible obs: 83.3 %
Reflection
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 15 Å / Rmerge(I) obs: 0.106

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.8→6 Å / Rfactor Rwork: 0.203 / Rfactor obs: 0.203 / σ(F): 2
Displacement parametersBiso mean: 28 Å2
Refinement stepCycle: LAST / Resolution: 2.8→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12358 0 0 0 12358
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.019
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.25
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it

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