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- PDB-7c9q: Crystal structure of Human liver fructose-1,6-bisphoaphatase comp... -

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Basic information

Entry
Database: PDB / ID: 7c9q
TitleCrystal structure of Human liver fructose-1,6-bisphoaphatase complex with Mg2+ and AMP
ComponentsFructose-1,6-bisphosphatase 1
KeywordsHYDROLASE / magnesium
Function / homology
Function and homology information


cellular response to raffinose / cellular hypotonic salinity response / fructose-bisphosphatase / cellular response to phorbol 13-acetate 12-myristate / fructose 1,6-bisphosphate 1-phosphatase activity / negative regulation of Ras protein signal transduction / fructose 1,6-bisphosphate metabolic process / cellular response to magnesium ion / Gluconeogenesis / fructose metabolic process ...cellular response to raffinose / cellular hypotonic salinity response / fructose-bisphosphatase / cellular response to phorbol 13-acetate 12-myristate / fructose 1,6-bisphosphate 1-phosphatase activity / negative regulation of Ras protein signal transduction / fructose 1,6-bisphosphate metabolic process / cellular response to magnesium ion / Gluconeogenesis / fructose metabolic process / fructose 6-phosphate metabolic process / monosaccharide binding / negative regulation of glycolytic process / regulation of gluconeogenesis / cellular hyperosmotic salinity response / AMP binding / cellular response to cAMP / gluconeogenesis / response to nutrient levels / negative regulation of cell growth / cellular response to xenobiotic stimulus / cellular response to insulin stimulus / RNA polymerase II-specific DNA-binding transcription factor binding / negative regulation of transcription by RNA polymerase II / extracellular exosome / metal ion binding / identical protein binding / nucleus / 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
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / Fructose-1,6-bisphosphatase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.878 Å
AuthorsHuang, Y. / Li, R. / Wan, J.
CitationJournal: To Be Published
Title: Crystal structure of Human liver fructose-1,6-bisphoaphatase complex with Mg2+ and AMP
Authors: Huang, Y. / Li, R. / Wan, J.
History
DepositionJun 7, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 9, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: 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

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Assembly

Deposited unit
A: Fructose-1,6-bisphosphatase 1
C: Fructose-1,6-bisphosphatase 1
D: Fructose-1,6-bisphosphatase 1
B: Fructose-1,6-bisphosphatase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,92412
Polymers147,4384
Non-polymers1,4868
Water13,457747
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18570 Å2
ΔGint-136 kcal/mol
Surface area44770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.361, 83.286, 276.544
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 36859.418 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FBP1, FBP / Production host: Escherichia coli (E. coli) / References: UniProt: P09467, fructose-bisphosphatase
#2: Chemical
ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 747 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.66 Å3/Da / Density % sol: 53.75 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 50mM Hepes pH 7.2, 150mM Sodium chloride, 8% (w/v) PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9791 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 14, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.878→39.506 Å / Num. obs: 126447 / % possible obs: 98.9 % / Redundancy: 3.8 % / CC1/2: 0.99 / Net I/σ(I): 14.76
Reflection shellResolution: 1.878→1.887 Å / Num. unique obs: 20795 / CC1/2: 0.835

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ZWK

5zwk


Resolution: 1.878→35.694 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2188 6322 5 %
Rwork0.1815 120114 -
obs0.1833 126436 98.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 80.87 Å2 / Biso mean: 31.6754 Å2 / Biso min: 13.83 Å2
Refinement stepCycle: final / Resolution: 1.878→35.694 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9895 0 96 747 10738
Biso mean--40.84 37.84 -
Num. residues----1295
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.878-1.89930.27771970.2385373794
1.8993-1.92170.28792080.2362395598
1.9217-1.94510.28952070.2303393898
1.9451-1.96970.2782060.2115391598
1.9697-1.99570.23252080.2012394599
1.9957-2.0230.26172070.1933393398
2.023-2.05190.2292080.1943396199
2.0519-2.08250.22842070.1971393598
2.0825-2.11510.23532100.20173989100
2.1151-2.14970.24292070.2013391698
2.1497-2.18680.24522100.1947399999
2.1868-2.22660.23412090.2029396299
2.2266-2.26940.25662070.2032395298
2.2694-2.31570.24082100.1953398399
2.3157-2.3660.22822100.19163986100
2.366-2.42110.2442090.1873397599
2.4211-2.48160.2392110.1919400299
2.4816-2.54870.24822100.1935398899
2.5487-2.62360.25412100.192399599
2.6236-2.70830.22312110.1942402099
2.7083-2.80510.24152140.1897405399
2.8051-2.91730.23822100.18563999100
2.9173-3.050.23032140.18514050100
3.05-3.21070.21032130.1756405899
3.2107-3.41170.21532120.17664025100
3.4117-3.67490.17712150.16514083100
3.6749-4.04430.19512160.16474104100
4.0443-4.62840.18392170.15024136100
4.6284-5.82720.1982200.16734173100
5.8272-35.69390.20472290.1817434799

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