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- PDB-5et7: Human muscle fructose-1,6-bisphosphatase in inactive T-state -

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Basic information

Entry
Database: PDB / ID: 5et7
TitleHuman muscle fructose-1,6-bisphosphatase in inactive T-state
ComponentsFructose-1,6-bisphosphatase isozyme 2
KeywordsHYDROLASE / carbohydrate metabolism / glyconeogenesis / muscle / FBPase / T-state
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: 2.989 Å
AuthorsBarciszewski, J. / Wisniewski, J. / Kolodziejczyk, R. / Dzugaj, A. / Jaskolski, M. / Rakus, D.
Funding support Poland, 1items
OrganizationGrant numberCountry
Polish National Science Center2013/09/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 1, 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 1.3Aug 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 1.4Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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
C: Fructose-1,6-bisphosphatase isozyme 2
B: Fructose-1,6-bisphosphatase isozyme 2
D: Fructose-1,6-bisphosphatase isozyme 2


Theoretical massNumber of molelcules
Total (without water)146,6684
Polymers146,6684
Non-polymers00
Water00
1
A: Fructose-1,6-bisphosphatase isozyme 2
B: Fructose-1,6-bisphosphatase isozyme 2

A: Fructose-1,6-bisphosphatase isozyme 2
B: Fructose-1,6-bisphosphatase isozyme 2


Theoretical massNumber of molelcules
Total (without water)146,6684
Polymers146,6684
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z1
2
C: Fructose-1,6-bisphosphatase isozyme 2
D: Fructose-1,6-bisphosphatase isozyme 2

C: Fructose-1,6-bisphosphatase isozyme 2
D: Fructose-1,6-bisphosphatase isozyme 2


Theoretical massNumber of molelcules
Total (without water)146,6684
Polymers146,6684
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556x,-y,-z+11
Unit cell
Length a, b, c (Å)218.510, 234.796, 71.853
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222

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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.: 4
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

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.62 Å3/Da / Density % sol: 66.04 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 1.6M ammonium citrate tribasic / PH range: 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Sep 8, 2012
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: 2.99→45.92 Å / Num. all: 37760 / Num. obs: 37760 / % possible obs: 99.4 % / Redundancy: 12.2 % / Biso Wilson estimate: 55.75 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 24.2
Reflection shellResolution: 2.99→3.17 Å / Redundancy: 12 % / Rmerge(I) obs: 0.82 / Mean I/σ(I) obs: 4.03 / % possible all: 97.4

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Processing

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

3ifa


Resolution: 2.989→45.458 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.27 / Stereochemistry target values: ENGH & HUBER / Details: H atoms were added at riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2443 999 2.65 %Random selection
Rwork0.177 ---
obs0.1789 37723 99.38 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.989→45.458 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8589 0 0 0 8589
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0158719
X-RAY DIFFRACTIONf_angle_d1.76711779
X-RAY DIFFRACTIONf_dihedral_angle_d16.853237
X-RAY DIFFRACTIONf_chiral_restr0.0681386
X-RAY DIFFRACTIONf_plane_restr0.0071476
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9894-3.1470.28951370.2155040X-RAY DIFFRACTION97
3.147-3.34410.26161400.19835173X-RAY DIFFRACTION100
3.3441-3.60220.24931430.17635232X-RAY DIFFRACTION100
3.6022-3.96450.26081420.16875244X-RAY DIFFRACTION100
3.9645-4.53770.22591430.15345240X-RAY DIFFRACTION100
4.5377-5.71520.21941450.16125317X-RAY DIFFRACTION100
5.7152-45.46360.24751490.19525478X-RAY DIFFRACTION99
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)
18.0904-1.648-0.47265.8089-0.28224.6617-0.2314-0.05650.7476-0.0863-0.0253-1.1029-0.68790.71710.2760.6533-0.1342-0.16810.42140.11870.653222.719347.98332.0331
22.1851-0.03420.26353.51750.34381.2796-0.1418-0.08390.1070.132-0.018-0.3358-0.21550.0110.17130.47630.0108-0.13820.39750.02890.256211.431829.77848.1565
36.84961.48960.42263.02051.45126.0725-0.1642-0.9714-0.17831.03930.261-0.62610.62090.3781-0.12160.89540.1175-0.3310.5559-0.06270.68698.591871.835620.0618
42.3691-0.010.81253.78090.20591.9277-0.1433-0.13660.90730.3870.0922-0.3727-0.18240.20280.02790.5397-0.0045-0.30990.5486-0.13761.107411.251890.18148.2136
56.5752-0.75591.61696.41160.10414.4508-0.2541-0.40420.82190.1346-0.2562-0.7216-0.80740.50070.49650.5222-0.1134-0.16280.59420.13990.603538.605220.985532.0511
65.08730.1008-0.11252.6767-0.7913.3451-0.1985-0.0650.18450.0676-0.0866-0.0995-0.2019-0.18750.28780.36260.0371-0.05820.40660.03760.201920.845110.314126.5634
72.28411.1053-0.13265.009-0.21724.6918-0.01160.8890.5208-0.57770.14660.2438-0.2129-0.61-0.12070.50950.01620.02250.94730.50140.961263.02366.849716.1087
83.4140.2749-0.57421.8578-0.17642.43520.08610.44020.3684-0.0716-0.1445-0.7453-0.15780.20950.03660.5213-0.03480.10670.61620.45651.23881.018210.639426.8679
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 11 through 155 )
2X-RAY DIFFRACTION2chain 'A' and (resid 156 through 336 )
3X-RAY DIFFRACTION3chain 'B' and (resid 11 through 155 )
4X-RAY DIFFRACTION4chain 'B' and (resid 156 through 334 )
5X-RAY DIFFRACTION5chain 'C' and (resid 11 through 155 )
6X-RAY DIFFRACTION6chain 'C' and (resid 156 through 334 )
7X-RAY DIFFRACTION7chain 'D' and (resid 11 through 155 )
8X-RAY DIFFRACTION8chain 'D' and (resid 156 through 334 )

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