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- PDB-5l0a: Human muscle fructose-1,6-bisphosphatase E69Q mutant in active R-... -

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Basic information

Entry
Database: PDB / ID: 5l0a
TitleHuman muscle fructose-1,6-bisphosphatase E69Q mutant in active R-state in complex with fructose-1,6-bisphosphate
ComponentsFructose-1,6-bisphosphatase isozyme 2
KeywordsHYDROLASE / carbohydrate metabolism / glyconeogenesis / muscle izoenzyme / FBPase / R-state / Leucine lock / E69Q / fructose-1 / 6-bisphosphate
Function / homology
Function and homology information


sucrose biosynthetic process / fructose-bisphosphatase / fructose 1,6-bisphosphate 1-phosphatase activity / fructose 1,6-bisphosphate metabolic process / fructose 6-phosphate metabolic process / Gluconeogenesis / fructose metabolic process / anchoring junction / gluconeogenesis / Z disc ...sucrose biosynthetic process / fructose-bisphosphatase / fructose 1,6-bisphosphate 1-phosphatase activity / fructose 1,6-bisphosphate metabolic process / fructose 6-phosphate metabolic process / Gluconeogenesis / fructose metabolic process / anchoring junction / gluconeogenesis / Z disc / extracellular exosome / identical protein binding / metal ion binding / nucleus / plasma membrane / 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
1,6-di-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: 2.302 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
#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.
#3: 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.
History
DepositionJul 27, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 16, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 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 1.2Jan 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)37,0062
Polymers36,6661
Non-polymers3401
Water21612
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)148,0248
Polymers146,6644
Non-polymers1,3604
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z1
crystal symmetry operation10_665-x+1,-y+1,z1
crystal symmetry operation15_555y,x,-z1
Buried area12060 Å2
ΔGint-73 kcal/mol
Surface area44720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.446, 72.446, 233.954
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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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: 36665.910 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Gaps in the sequence indicate residues that were not modeled because of poor electron density
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-FBP / 1,6-di-O-phosphono-beta-D-fructofuranose / BETA-FRUCTOSE-1,6-DIPHOSPHATE / FRUCTOSE-1,6-BISPHOSPHATE / 1,6-di-O-phosphono-beta-D-fructose / 1,6-di-O-phosphono-D-fructose / 1,6-di-O-phosphono-fructose / Fructose 1,6-bisphosphate


Type: D-saccharide, beta linking / Mass: 340.116 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H14O12P2
IdentifierTypeProgram
b-D-Fruf1PO36PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 2.09 Å3/Da / Density % sol: 41.23 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 10mM magnesium chloride, 2M sodium chloride, 10%PEG6000, 10mM Tris

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.3 / Wavelength: 0.8943 Å
DetectorType: RAYONIX SX-165mm / Detector: CCD / Date: Jun 27, 2010
RadiationMonochromator: Double Crystal Monochromator, Si-111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8943 Å / Relative weight: 1
ReflectionResolution: 2.3→31.03 Å / Num. obs: 13949 / % possible obs: 93.9 % / Redundancy: 8.7 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 3.49
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.622 / Mean I/σ(I) obs: 2 / % possible all: 69.5

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ET5

5et5


Resolution: 2.302→31.027 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 32.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.288 931 7.15 %Random selection
Rwork0.215 ---
obs0.2203 13014 90.64 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.302→31.027 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2133 0 20 12 2165
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092196
X-RAY DIFFRACTIONf_angle_d1.2232974
X-RAY DIFFRACTIONf_dihedral_angle_d14.791824
X-RAY DIFFRACTIONf_chiral_restr0.041349
X-RAY DIFFRACTIONf_plane_restr0.006369
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3015-2.42280.35681060.28231271X-RAY DIFFRACTION69
2.4228-2.57450.34881270.28561612X-RAY DIFFRACTION87
2.5745-2.77320.37061220.26531742X-RAY DIFFRACTION93
2.7732-3.0520.32451350.26681755X-RAY DIFFRACTION94
3.052-3.49320.28411310.23011847X-RAY DIFFRACTION97
3.4932-4.3990.25751700.18541834X-RAY DIFFRACTION97
4.399-31.02960.26991400.18772022X-RAY DIFFRACTION98
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)
12.67830.26560.41653.0115-1.55174.60910.2188-0.48380.24241.0858-0.3591-0.779-0.56580.35930.10790.6954-0.2099-0.19620.46460.01030.650223.665334.222619.0622
22.24850.71970.69624.56050.5762.83270.0795-0.19410.3890.3217-0.1182-0.3794-0.34020.05650.0470.3254-0.0698-0.00890.2880.02220.461913.404733.46269.0105
32.94420.451-0.04835.71211.02823.50410.1305-0.1552-0.07790.4927-0.1160.63010.1738-0.2114-0.05350.2722-0.06410.05870.25950.04260.41924.491618.52599.7669
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 9 through 139 )
2X-RAY DIFFRACTION2chain 'A' and (resid 149 through 212 )
3X-RAY DIFFRACTION3chain 'A' and (resid 213 through 334 )

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