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- PDB-2ox3: R-state, PEP and Fru-6-P-bound, Escherichia coli fructose-1,6-bis... -

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Basic information

Entry
Database: PDB / ID: 2ox3
TitleR-state, PEP and Fru-6-P-bound, Escherichia coli fructose-1,6-bisphosphatase
ComponentsFructose-1,6-bisphosphataseFructose 1,6-bisphosphatase
KeywordsHYDROLASE / Glycolysis / Gluconeogenesis / Bacteria / Carbohydrate Metabolism / Diabetes / Protein-protein Interactions / Proteobacteria / Gram-negative / Protein Crystallography
Function / homology
Function and homology information


sucrose biosynthetic process / fructose-bisphosphatase / fructose 1,6-bisphosphate 1-phosphatase activity / fructose 6-phosphate metabolic process / fructose metabolic process / fructose 1,6-bisphosphate metabolic process / gluconeogenesis / nucleotide binding / magnesium ion binding / protein-containing complex ...sucrose biosynthetic process / fructose-bisphosphatase / fructose 1,6-bisphosphate 1-phosphatase activity / fructose 6-phosphate metabolic process / fructose metabolic process / fructose 1,6-bisphosphate metabolic process / gluconeogenesis / nucleotide binding / magnesium ion binding / protein-containing complex / identical protein binding / 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 / PHOSPHOENOLPYRUVATE / Fructose-1,6-bisphosphatase class 1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.18 Å
AuthorsHines, J.K. / Fromm, H.J. / Honzatko, R.B.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Structures of activated fructose-1,6-bisphosphatase from Escherichia coli. Coordinate regulation of bacterial metabolism and the conservation of the R-state.
Authors: Hines, J.K. / Fromm, H.J. / Honzatko, R.B.
History
DepositionFeb 19, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.contact_author / _software.contact_author_email ..._software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_ref_seq_dif / 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_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Aug 30, 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
Revision 1.6Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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)37,5893
Polymers37,1611
Non-polymers4282
Water1,44180
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)150,35812
Polymers148,6454
Non-polymers1,7138
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
Unit cell
Length a, b, c (Å)44.687, 83.112, 174.422
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-511-

HOH

DetailsBiological unit is a tetramer constructed from the monomer using the following rotational symmetry operators: (x,y,z), (-x,-y,z), (x,-y,-z), (-x,y,-z)

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Components

#1: Protein Fructose-1,6-bisphosphatase / Fructose 1,6-bisphosphatase / D-fructose-1 / 6-bisphosphate 1-phosphohydrolase / FBPase


Mass: 37161.234 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: XL1-Blue / Gene: fbp, fdp / Plasmid: pET-24b / Production host: Escherichia coli (E. coli) / Strain (production host): DF657 / References: UniProt: P0A993, 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.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H13O9P
IdentifierTypeProgram
b-D-Fruf6PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical ChemComp-PEP / PHOSPHOENOLPYRUVATE / Phosphoenolpyruvic acid


Mass: 168.042 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5O6P
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 80 / 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: 2.18 Å3/Da / Density % sol: 43.53 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 50 mM sodium acetate, pH 5.6, 16% (w/v) PEG 1500, and 20% (w/v) sucrose, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54
DetectorDetector: IMAGE PLATE / Date: Sep 13, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.18→75.03 Å / Num. all: 17261 / Num. obs: 17261 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Biso Wilson estimate: 23.1 Å2 / Rmerge(I) obs: 0.046 / Rsym value: 0.046 / Net I/σ(I): 21.1
Reflection shellResolution: 2.18→2.32 Å / Redundancy: 6 % / Rmerge(I) obs: 0.238 / Mean I/σ(I) obs: 6.8 / Num. unique all: 2657 / Rsym value: 0.238 / % possible all: 92.8

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Processing

Software
NameVersionClassificationNB
CNS1.1refinement
PDB_EXTRACT2data extraction
CrystalClear(MSC/RIGAKU)data collection
d*TREKdata reduction
d*TREKdata scaling
AMoREphasing
REFMACrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID: 2GQ1

2gq1


Resolution: 2.18→75.03 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 3458218 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.262 1719 10 %RANDOM
Rwork0.212 ---
all0.216 17261 --
obs0.216 17261 98.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 42.72 Å2 / ksol: 0.351 e/Å3
Displacement parametersBiso mean: 39.4 Å2
Baniso -1Baniso -2Baniso -3
1-2.66 Å20 Å20 Å2
2--6.85 Å20 Å2
3----9.51 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.37 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 2.18→75.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2476 0 26 80 2582
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d22.5
X-RAY DIFFRACTIONc_improper_angle_d0.75
X-RAY DIFFRACTIONc_mcbond_it1.41.5
X-RAY DIFFRACTIONc_mcangle_it2.312
X-RAY DIFFRACTIONc_scbond_it2.192
X-RAY DIFFRACTIONc_scangle_it2.892.5
LS refinement shellResolution: 2.18→2.32 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.357 299 11.3 %
Rwork0.322 2358 -
obs-2657 92.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4lig.paramlig.top
X-RAY DIFFRACTION5PEP.paramPEP.top

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