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- PDB-1cnq: FRUCTOSE-1,6-BISPHOSPHATASE COMPLEXED WITH FRUCTOSE-6-PHOSPHATE A... -

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Basic information

Entry
Database: PDB / ID: 1cnq
TitleFRUCTOSE-1,6-BISPHOSPHATASE COMPLEXED WITH FRUCTOSE-6-PHOSPHATE AND ZINC IONS
ComponentsFRUCTOSE-1,6-BISPHOSPHATASEFructose 1,6-bisphosphatase
KeywordsHYDROLASE / BISPHOSPHATASE
Function / homology
Function and homology information


Gluconeogenesis / sucrose biosynthetic process / fructose-bisphosphatase / fructose 1,6-bisphosphate 1-phosphatase activity / negative regulation of Ras protein signal transduction / fructose 1,6-bisphosphate metabolic process / cellular response to magnesium ion / fructose 6-phosphate metabolic process / fructose metabolic process / monosaccharide binding ...Gluconeogenesis / sucrose biosynthetic process / fructose-bisphosphatase / fructose 1,6-bisphosphate 1-phosphatase activity / negative regulation of Ras protein signal transduction / fructose 1,6-bisphosphate metabolic process / cellular response to magnesium ion / fructose 6-phosphate metabolic process / fructose metabolic process / monosaccharide binding / negative regulation of glycolytic process / regulation of gluconeogenesis / AMP binding / dephosphorylation / 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 / identical protein binding / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Fructose-1,6-bisphosphatase / Fructose-1,6-bisphosphatase, active site / Fructose-1-6-bisphosphatase class 1, C-terminal / Fructose-1-6-bisphosphatase active site. / Fructose-1,6-bisphosphatase class 1 / Fructose-1-6-bisphosphatase class I, N-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 class 1, C-terminal / Fructose-1-6-bisphosphatase active site. / Fructose-1,6-bisphosphatase class 1 / Fructose-1-6-bisphosphatase class I, N-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 / MOLECULAR REPLACEMENT / Resolution: 2.27 Å
AuthorsChoe, J. / Poland, B.W. / Fromm, H. / Honzatko, R.
CitationJournal: Biochemistry / Year: 1998
Title: Role of a dynamic loop in cation activation and allosteric regulation of recombinant porcine fructose-1,6-bisphosphatase.
Authors: Choe, J.Y. / Poland, B.W. / Fromm, H.J. / Honzatko, R.B.
History
DepositionMay 21, 1999Processing site: BNL
SupersessionMay 28, 1999ID: 1BFL
Revision 1.0May 28, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / 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 1.4Aug 9, 2023Group: Database references / Refinement description / Structure summary
Category: chem_comp / 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

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Assembly

Deposited unit
A: FRUCTOSE-1,6-BISPHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5037
Polymers36,6911
Non-polymers8116
Water2,504139
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)150,01128
Polymers146,7654
Non-polymers3,24624
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 area20520 Å2
ΔGint-611 kcal/mol
Surface area43580 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)52.340, 82.820, 166.740
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein FRUCTOSE-1,6-BISPHOSPHATASE / Fructose 1,6-bisphosphatase / FBPASE


Mass: 36691.207 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Organ: LIVER / Production host: Escherichia coli (E. coli) / Strain (production host): DF657 / 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 / Fructose 6-phosphate


Type: D-saccharide, beta linking / Mass: 260.136 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H13O9P
IdentifierTypeProgram
b-D-Fruf6PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 139 / 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: 2.46 Å3/Da / Density % sol: 50.03 %
Crystal growpH: 7.4 / Details: pH 7.4
Crystal grow
*PLUS
Temperature: 37 ℃ / Method: vapor diffusion, hanging drop
Details: drop consists of equal volume of protein and reservoir solutions
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
22.5 mMTris-malonate1drop
310 mM1dropKPi
45 mM1dropZnCl2
55 mMF6P1drop
62.5 mMTris-malonate1reservoir
76 %(w/v)PEG33501reservoir

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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: Dec 1, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.27→99 Å / Num. obs: 15519 / % possible obs: 90 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.055
Reflection shellResolution: 2.27→2.4 Å / % possible all: 56
Reflection shell
*PLUS
% possible obs: 56 %

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Processing

Software
NameVersionClassification
CNS0.5refinement
XENGENdata reduction
XENGENdata scaling
CNS0.5phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FBE

1fbe


Resolution: 2.27→5 Å / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.227 1339 10 %RANDOM
Rwork0.168 ---
obs0.168 13386 77.6 %-
Displacement parametersBiso mean: 29.7 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.27→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2537 0 40 139 2716
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.47
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.16
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.2
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARNAH1E.DNATOPH19.PEP
X-RAY DIFFRACTION3PARAM19.SOL
Software
*PLUS
Name: CNS / Version: 0.5 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.16
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.2

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