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- PDB-5et8: Human muscle fructose-1,6-bisphosphatase in active R-state in com... -

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Basic information

Entry
Database: PDB / ID: 5et8
TitleHuman muscle fructose-1,6-bisphosphatase in active R-state in complex with fructose-6-phosphate
ComponentsFructose-1,6-bisphosphatase isozyme 2
KeywordsHYDROLASE / carbohydrate metabolism / glyconeogenesis / muscle / FBPase / R-state / Leucine lock / Asp187 / fructose-6-phosphate
Function / homology
Function and homology information


sucrose biosynthetic process / fructose-bisphosphatase / fructose 1,6-bisphosphate 1-phosphatase activity / fructose 6-phosphate metabolic process / Gluconeogenesis / fructose metabolic process / fructose 1,6-bisphosphate metabolic process / anchoring junction / gluconeogenesis / Z disc ...sucrose biosynthetic process / fructose-bisphosphatase / fructose 1,6-bisphosphate 1-phosphatase activity / fructose 6-phosphate metabolic process / Gluconeogenesis / fructose metabolic process / fructose 1,6-bisphosphate metabolic process / anchoring junction / gluconeogenesis / Z disc / extracellular exosome / identical protein binding / nucleus / metal ion binding / plasma membrane / cytoplasm / cytosol
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 / Fructose-1,6-bisphosphatase isozyme 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
AuthorsBarciszewski, J. / Wisniewski, J. / Kolodziejczyk, R. / Dzugaj, A. / Jaskolski, M. / Rakus, D.
Funding support Poland, 1items
OrganizationGrant numberCountry
Polish National Science Centre2013/09/B/NZ1/01081 Poland
Citation
Journal: To Be Published
Title: T-to-R switch of muscle FBPase involves extreme changes of secondary and quaternary structure
Authors: Barciszewski, J. / Wisniewski, J. / Kolodziejczyk, R. / Dzugaj, A. / Jaskolski, M. / Rakus, D.
#1: Journal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2011
Title: Structure of E69Q mutant of human muscle fructose-1,6-bisphosphatase.
Authors: Zarzycki, M. / Kolodziejczyk, R. / Maciaszczyk-Dziubinska, E. / Wysocki, R. / Jaskolski, M. / Dzugaj, A.
#2: Journal: PLoS ONE / Year: 2013
Title: Crystal structures of human muscle fructose-1,6-bisphosphatase: novel quaternary states, enhanced AMP affinity, and allosteric signal transmission pathway.
Authors: Shi, R. / Chen, Z.Y. / Zhu, D.W. / Li, C. / Shan, Y. / Xu, G. / Lin, S.X.
History
DepositionNov 17, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Nov 23, 2016Provider: repository / Type: Initial release
Revision 2.0Aug 8, 2018Group: Atomic model / Data collection / Database references / Category: atom_site / pdbx_related_exp_data_set
Item: _atom_site.occupancy / _pdbx_related_exp_data_set.data_reference / _pdbx_related_exp_data_set.metadata_reference
Revision 2.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / 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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.2Jan 10, 2024Group: 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 isozyme 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9272
Polymers36,6671
Non-polymers2601
Water1,69394
1
A: Fructose-1,6-bisphosphatase isozyme 2
hetero molecules

A: Fructose-1,6-bisphosphatase isozyme 2
hetero molecules

A: Fructose-1,6-bisphosphatase isozyme 2
hetero molecules

A: Fructose-1,6-bisphosphatase isozyme 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,7088
Polymers146,6684
Non-polymers1,0414
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z1
crystal symmetry operation10_555-x,-y,z1
crystal symmetry operation15_555y,x,-z1
Buried area11760 Å2
ΔGint-63 kcal/mol
Surface area45180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.105, 72.105, 232.002
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-536-

HOH

21A-592-

HOH

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Components

#1: Protein Fructose-1,6-bisphosphatase isozyme 2 / FBPase 2 / D-fructose-1 / 6-bisphosphate 1-phosphohydrolase 2 / Muscle FBPase


Mass: 36666.895 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue: skeletal muscle / Gene: FBP2 / Plasmid: pKK223-3 / Production host: Escherichia coli (E. coli) / Strain (production host): C100 / References: UniProt: O00757, 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.06 Å3/Da / Density % sol: 59.9 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 10mM magnesium chloride, 2M sodium chloride, 10%PEG6000, 10mM Tris
PH range: 7.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jan 22, 2010
RadiationMonochromator: Double Crystal Monochromator, Si-111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.92→46.69 Å / Num. all: 23929 / Num. obs: 23929 / % possible obs: 99.8 % / Redundancy: 9.57 % / Biso Wilson estimate: 38.32 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 19.05
Reflection shellResolution: 1.92→2.04 Å / Redundancy: 9.76 % / Rmerge(I) obs: 0.9 / Mean I/σ(I) obs: 2.57 / % possible all: 99.4

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIX1.8.4_1496refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3IFA

3ifa


Resolution: 1.92→46.676 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / Phase error: 23.56 / Stereochemistry target values: ENGH & HUBER / Details: Hydrogen atoms were added at riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2233 1028 4.3 %Random selection
Rwork0.1796 ---
obs0.1815 23927 99.81 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.69 Å2
Refinement stepCycle: LAST / Resolution: 1.92→46.676 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2201 0 16 94 2311
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0182277
X-RAY DIFFRACTIONf_angle_d1.7113082
X-RAY DIFFRACTIONf_dihedral_angle_d16.43856
X-RAY DIFFRACTIONf_chiral_restr0.078363
X-RAY DIFFRACTIONf_plane_restr0.008383
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9196-2.02080.30161420.24643169X-RAY DIFFRACTION99
2.0208-2.14740.29161450.20853218X-RAY DIFFRACTION100
2.1474-2.31330.28171450.1963233X-RAY DIFFRACTION100
2.3133-2.5460.27391450.19953232X-RAY DIFFRACTION100
2.546-2.91440.25691470.19143262X-RAY DIFFRACTION100
2.9144-3.67160.20861480.17973304X-RAY DIFFRACTION100
3.6716-46.69010.18221560.15683481X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.06930.7897-0.31484.8568-4.2663.83890.2797-0.1590.17530.8461-0.1543-0.3125-0.82920.4582-0.13680.393-0.1263-0.06620.3079-0.05280.5321-12.23075.561710.3177
25.8353-0.1121-0.43422.64251.8836.40990.1785-0.60290.4481.0019-0.2008-0.6946-0.36630.3178-0.03460.6411-0.1145-0.21460.4045-0.01670.3906-11.5816-4.827824.8098
34.5984-0.3829-2.23053.2283-0.3026.87930.0476-0.11030.23540.5608-0.1221-0.2808-0.18560.17340.02640.2576-0.0426-0.06740.1564-0.04270.3329-19.6288-1.868213.5136
41.96960.2616-0.04343.96140.93362.29630.0468-0.10460.03470.3124-0.02090.29420.0811-0.1619-0.020.1574-0.00220.03470.16790.01210.2014-31.5495-16.77918.5938
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 9 through 49 )
2X-RAY DIFFRACTION2chain 'A' and (resid 50 through 118 )
3X-RAY DIFFRACTION3chain 'A' and (resid 119 through 197 )
4X-RAY DIFFRACTION4chain 'A' and (resid 198 through 334)

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