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- PDB-5et5: Human muscle fructose-1,6-bisphosphatase in active R-state -

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Basic information

Entry
Database: PDB / ID: 5et5
TitleHuman muscle fructose-1,6-bisphosphatase in active R-state
ComponentsFructose-1,6-bisphosphatase isozyme 2
KeywordsHYDROLASE / carbohydrate metabolism / glyconeogenesis / muscle / FBPase / R-state / Leucine lock / Asp187
Function / homology
Function and homology information


fructose-bisphosphatase / fructose 1,6-bisphosphate 1-phosphatase activity / fructose 1,6-bisphosphate metabolic process / Gluconeogenesis / fructose metabolic process / fructose 6-phosphate metabolic process / anchoring junction / gluconeogenesis / Z disc / extracellular exosome ...fructose-bisphosphatase / fructose 1,6-bisphosphate 1-phosphatase activity / fructose 1,6-bisphosphate metabolic process / Gluconeogenesis / fructose metabolic process / fructose 6-phosphate metabolic process / anchoring junction / gluconeogenesis / Z disc / extracellular exosome / metal ion binding / identical protein binding / nucleus / plasma membrane / 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 isozyme 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.67 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: Acta Crystallogr D Struct Biol / Year: 2016
Title: T-to-R switch of muscle fructose-1,6-bisphosphatase involves fundamental changes of secondary and quaternary structure.
Authors: Barciszewski, J. / Wisniewski, J. / Kolodziejczyk, R. / Jaskolski, M. / Rakus, D. / Dzugaj, A.
#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 1.0Apr 13, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 20, 2016Group: Database references
Revision 1.2Aug 8, 2018Group: Data collection / Database references / Category: pdbx_related_exp_data_set
Item: _pdbx_related_exp_data_set.data_reference / _pdbx_related_exp_data_set.metadata_reference
Revision 1.3Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
Item: _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 isozyme 2


Theoretical massNumber of molelcules
Total (without water)36,6671
Polymers36,6671
Non-polymers00
Water2,396133
1
A: Fructose-1,6-bisphosphatase isozyme 2

A: Fructose-1,6-bisphosphatase isozyme 2

A: Fructose-1,6-bisphosphatase isozyme 2

A: Fructose-1,6-bisphosphatase isozyme 2


Theoretical massNumber of molelcules
Total (without water)146,6684
Polymers146,6684
Non-polymers00
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 area9880 Å2
ΔGint-62 kcal/mol
Surface area45250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.564, 72.564, 235.348
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-418-

HOH

21A-523-

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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 133 / 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: 2.07 Å3/Da / Density % sol: 40.49 %
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: 1.67→36.28 Å / Num. all: 37062 / Num. obs: 37062 / % possible obs: 99.8 % / Redundancy: 13.03 % / Biso Wilson estimate: 24.92 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 29.89
Reflection shellResolution: 1.67→1.77 Å / Redundancy: 13.18 % / Rmerge(I) obs: 0.9 / Mean I/σ(I) obs: 3.08 / % 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: 1.67→36.28 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / Phase error: 23.23 / Stereochemistry target values: ENGH & HUBER / Details: H ATOMS WERE ADDED AT RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2196 1001 2.7 %Random selection
Rwork0.1933 ---
obs0.194 37060 99.78 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.09 Å2
Refinement stepCycle: LAST / Resolution: 1.67→36.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2166 0 0 133 2299
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0192217
X-RAY DIFFRACTIONf_angle_d1.7912996
X-RAY DIFFRACTIONf_dihedral_angle_d14.665825
X-RAY DIFFRACTIONf_chiral_restr0.094356
X-RAY DIFFRACTIONf_plane_restr0.01374
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6689-1.75680.27231390.23735026X-RAY DIFFRACTION99
1.7568-1.86690.27281420.22485105X-RAY DIFFRACTION100
1.8669-2.0110.27481400.23765059X-RAY DIFFRACTION100
2.011-2.21340.22651420.19295103X-RAY DIFFRACTION100
2.2134-2.53360.25711420.20335131X-RAY DIFFRACTION100
2.5336-3.19180.21551450.19895202X-RAY DIFFRACTION100
3.1918-36.29060.18791510.1745433X-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)
11.92450.3482-0.48195.266-3.96433.79610.1902-0.0526-0.06330.77-0.1883-0.399-0.60850.1511-0.0160.3643-0.1137-0.07840.2555-0.01590.4677-12.25085.30569.6408
24.1742-0.4765-1.55884.19843.60384.68040.0749-0.4289-0.06040.81770.01-1.00460.1640.3403-0.22150.5909-0.1768-0.38370.34940.08020.6309-6.7475-7.483120.1749
33.60130.33390.11361.12990.56382.95860.0769-0.48250.40911.3058-0.1731-0.8445-0.30190.186-0.0990.7959-0.1246-0.20010.2527-0.00870.3617-15.8197-4.545924.8106
46.5433-0.4889-2.92632.3080.88575.97980.2171-0.81260.38040.9199-0.0096-0.1255-0.33530.0117-0.10260.532-0.0384-0.00990.219-0.02650.2806-24.6993-3.896822.5114
51.3890.45480.26943.92470.25441.01320.00740.09090.0889-0.0003-0.03070.0882-0.034-0.01360.02580.1147-0.0240.02030.17450.03030.1512-27.4168-12.77552.8497
62.37750.32750.36143.54130.7022.37320.0929-0.12150.04260.5263-0.0070.20310.1031-0.0908-0.06440.2238-0.04980.0530.14160.01220.1832-30.3888-14.351713.2159
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 8 through 50 )
2X-RAY DIFFRACTION2chain 'A' and (resid 51 through 88 )
3X-RAY DIFFRACTION3chain 'A' and (resid 89 through 139 )
4X-RAY DIFFRACTION4chain 'A' and (resid 140 through 167 )
5X-RAY DIFFRACTION5chain 'A' and (resid 168 through 247 )
6X-RAY DIFFRACTION6chain 'A' and (resid 248 through 331 )

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