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- PDB-1eyi: FRUCTOSE-1,6-BISPHOSPHATASE COMPLEX WITH MAGNESIUM, FRUCTOSE-6-PH... -

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Basic information

Entry
Database: PDB / ID: 1eyi
TitleFRUCTOSE-1,6-BISPHOSPHATASE COMPLEX WITH MAGNESIUM, FRUCTOSE-6-PHOSPHATE AND PHOSPHATE (R-STATE)
ComponentsFRUCTOSE-1,6-BISPHOSPHATASE
KeywordsHYDROLASE / bisphosphatase / allosteric enzymes / gluconeogenesis
Function / homology
Function and homology information


Gluconeogenesis / fructose-bisphosphatase / fructose 1,6-bisphosphate 1-phosphatase activity / cellular response to magnesium ion / fructose 1,6-bisphosphate metabolic process / negative regulation of Ras protein signal transduction / monosaccharide binding / fructose metabolic process / fructose 6-phosphate metabolic process / negative regulation of glycolytic process ...Gluconeogenesis / fructose-bisphosphatase / fructose 1,6-bisphosphate 1-phosphatase activity / cellular response to magnesium ion / fructose 1,6-bisphosphate metabolic process / negative regulation of Ras protein signal transduction / monosaccharide binding / fructose metabolic process / fructose 6-phosphate metabolic process / negative regulation of glycolytic process / regulation of gluconeogenesis / dephosphorylation / AMP binding / gluconeogenesis / negative regulation of cell growth / cellular response to xenobiotic stimulus / RNA polymerase II-specific DNA-binding transcription factor binding / negative regulation of transcription by RNA polymerase II / metal ion binding / identical protein binding / nucleus / cytosol / cytoplasm
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
6-O-phosphono-beta-D-fructofuranose / PHOSPHATE ION / Fructose-1,6-bisphosphatase 1
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / Resolution: 2.32 Å
AuthorsChoe, J. / Honzatko, R.B.
CitationJournal: Biochemistry / Year: 2000
Title: Crystal structures of fructose 1,6-bisphosphatase: mechanism of catalysis and allosteric inhibition revealed in product complexes.
Authors: Choe, J.Y. / Fromm, H.J. / Honzatko, R.B.
History
DepositionMay 6, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 9, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Nov 20, 2019Group: Derived calculations / Category: pdbx_struct_conn_angle / struct_conn
Revision 1.5Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.6Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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: FRUCTOSE-1,6-BISPHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1906
Polymers36,6911
Non-polymers4995
Water2,954164
1
A: FRUCTOSE-1,6-BISPHOSPHATASE
hetero molecules

A: FRUCTOSE-1,6-BISPHOSPHATASE
hetero molecules

A: FRUCTOSE-1,6-BISPHOSPHATASE
hetero molecules

A: FRUCTOSE-1,6-BISPHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,76024
Polymers146,7654
Non-polymers1,99520
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
Buried area17870 Å2
ΔGint-216 kcal/mol
Surface area44570 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)52.12, 82.51, 165.49
Angle α, β, γ (deg.)90, 90, 90
Int Tables number23
Space group name H-MI222

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Components

#1: Protein FRUCTOSE-1,6-BISPHOSPHATASE


Mass: 36691.207 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Tissue: LIVER / Plasmid: DF657 / Production host: Escherichia coli (E. coli) / References: UniProt: P00636, fructose-bisphosphatase
#2: Sugar ChemComp-F6P / 6-O-phosphono-beta-D-fructofuranose / FRUCTOSE-6-PHOSPHATE / 6-O-phosphono-beta-D-fructose / 6-O-phosphono-D-fructose / 6-O-phosphono-fructose


Type: D-saccharide, beta linking / Mass: 260.136 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H13O9P
IdentifierTypeProgram
b-D-Fruf6PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / 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: 2.4 Å3/Da / Density % sol: 48.44 %
Crystal growTemperature: 310 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 3350, HEPES, MPD, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 310K
Crystal grow
*PLUS
Temperature: 37 ℃ / pH: 7.4
Details: drop consists of equal volume of protein and reservoir solutions
Components of the solutions
*PLUS

Crystal-ID: 1

IDConc.UnitCommon nameSol-IDChemical formulaDetails
110 mg/mlproteindrop
210 mMdropKPi
35 mMdropZnCl2or 5 mM MgCl2
4mMF6Pdrop
5mMTris-malonatereservoir
6%(w/v)PEG3350reservoir

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Aug 1, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.32→50 Å / Num. all: 31247 / Num. obs: 30028 / % possible obs: 96.1 % / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Biso Wilson estimate: 16.2 Å2 / Rmerge(I) obs: 0.64 / Net I/σ(I): 15.6
Reflection shellResolution: 2.32→2.46 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.239 / Num. unique all: 3557 / % possible all: 75.5
Reflection
*PLUS
Num. measured all: 72680
Reflection shell
*PLUS
% possible obs: 75.5 %

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Processing

Software
NameClassification
CNSrefinement
X-GENdata reduction
X-GENdata scaling
CNSphasing
RefinementStarting model: 1CNQ

1cnq


Resolution: 2.32→5 Å / Rfactor Rfree error: 0.007 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.242 1280 10 %RANDOM
Rwork0.19 ---
obs-12784 91.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 132.213 Å2 / ksol: 1.47526 e/Å3
Displacement parametersBiso mean: 22.9 Å2
Baniso -1Baniso -2Baniso -3
1-8.36 Å20 Å20 Å2
2---5.37 Å20 Å2
3----2.99 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.36 Å0.28 Å
Refinement stepCycle: LAST / Resolution: 2.32→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2526 0 28 164 2718
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d22.6
X-RAY DIFFRACTIONc_improper_angle_d0.76
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.32→2.45 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.37 118 9.2 %
Rwork0.32 1170 -
obs--54.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
Software
*PLUS
Name: 'CNS' / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.76

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