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- PDB-4mjo: Human liver fructose-1,6-bisphosphatase(d-fructose-1,6-bisphospha... -

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Basic information

Entry
Database: PDB / ID: 4mjo
TitleHuman liver fructose-1,6-bisphosphatase(d-fructose-1,6-bisphosphate, 1-phosphohydrolase) (e.c.3.1.3.11) complexed with the allosteric inhibitor 3
ComponentsFructose-1,6-bisphosphatase 1
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Allostery / HYDROLASE (PHOSPHORIC MONOESTER) / HYDROLASE-HYDROLASE INHIBITOR complex
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 / 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
Chem-2C1 / Fructose-1,6-bisphosphatase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsRuf, A. / Joseph, C. / Tetaz, T. / Benz, J.
CitationJournal: Acs Chem.Biol. / Year: 2014
Title: Determination of protein-ligand binding constants of a cooperatively regulated tetrameric enzyme using electrospray mass spectrometry.
Authors: Cubrilovic, D. / Haap, W. / Barylyuk, K. / Ruf, A. / Badertscher, M. / Gubler, M. / Tetaz, T. / Joseph, C. / Benz, J. / Zenobi, R.
History
DepositionSep 4, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2014Group: Database references
Revision 1.2Apr 25, 2018Group: Advisory / Data collection / Source and taxonomy / Category: database_PDB_caveat / entity_src_nat / Item: _database_PDB_caveat.text
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fructose-1,6-bisphosphatase 1
B: Fructose-1,6-bisphosphatase 1
C: Fructose-1,6-bisphosphatase 1
D: Fructose-1,6-bisphosphatase 1
E: Fructose-1,6-bisphosphatase 1
F: Fructose-1,6-bisphosphatase 1
G: Fructose-1,6-bisphosphatase 1
H: Fructose-1,6-bisphosphatase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)299,15116
Polymers295,0998
Non-polymers4,0518
Water11,908661
1
A: Fructose-1,6-bisphosphatase 1
B: Fructose-1,6-bisphosphatase 1
C: Fructose-1,6-bisphosphatase 1
D: Fructose-1,6-bisphosphatase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,5758
Polymers147,5504
Non-polymers2,0264
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16110 Å2
ΔGint-79 kcal/mol
Surface area44390 Å2
MethodPISA
2
E: Fructose-1,6-bisphosphatase 1
F: Fructose-1,6-bisphosphatase 1
G: Fructose-1,6-bisphosphatase 1
H: Fructose-1,6-bisphosphatase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,5758
Polymers147,5504
Non-polymers2,0264
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16120 Å2
ΔGint-80 kcal/mol
Surface area44210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.974, 286.305, 83.692
Angle α, β, γ (deg.)90.00, 97.79, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16A
26G
17A
27H
18B
28C
19B
29D
110B
210E
111B
211F
112B
212G
113B
213H
114C
214D
115C
215E
116C
216F
117C
217G
118C
218H
119D
219E
120D
220F
121D
221G
122D
222H
123E
223F
124E
224G
125E
225H
126F
226G
127F
227H
128G
228H

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: SER / End label comp-ID: SER / Refine code: _ / Auth seq-ID: 9 - 335 / Label seq-ID: 10 - 336

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14AA
24EE
15AA
25FF
16AA
26GG
17AA
27HH
18BB
28CC
19BB
29DD
110BB
210EE
111BB
211FF
112BB
212GG
113BB
213HH
114CC
214DD
115CC
215EE
116CC
216FF
117CC
217GG
118CC
218HH
119DD
219EE
120DD
220FF
121DD
221GG
122DD
222HH
123EE
223FF
124EE
224GG
125EE
225HH
126FF
226GG
127FF
227HH
128GG
228HH

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28

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Components

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


Mass: 36887.434 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Organ: LIVER / References: UniProt: P09467, fructose-bisphosphatase
#2: Chemical
ChemComp-2C1 / N-({4-bromo-6-[(methylcarbamoyl)amino]pyridin-2-yl}carbamoyl)-5-(2-methoxyethyl)-4-methylthiophene-2-sulfonamide


Mass: 506.395 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C16H20BrN5O5S2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 661 / 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: 2.66 Å3/Da / Density % sol: 53.69 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M ammonium acetate and 12% polyethylenglycol 3350 in 0.1 M HEPES, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 300K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 16, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→30.5 Å / Num. all: 119425 / Num. obs: 115242 / % possible obs: 96.5 %

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Processing

SoftwareName: REFMAC / Version: 5.2.0019 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VT5

2vt5


Resolution: 2.4→29.74 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.905 / SU B: 10.168 / SU ML: 0.225 / Cross valid method: THROUGHOUT / ESU R: 0.436 / ESU R Free: 0.252 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23647 5784 5 %RANDOM
Rwork0.20664 ---
obs0.20817 109458 96.52 %-
all-115242 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.597 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å2-0.33 Å2
2--0.48 Å20 Å2
3----0.37 Å2
Refinement stepCycle: LAST / Resolution: 2.4→29.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19457 0 232 661 20350
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01920074
X-RAY DIFFRACTIONr_bond_other_d0.0080.0219609
X-RAY DIFFRACTIONr_angle_refined_deg1.5212.00127116
X-RAY DIFFRACTIONr_angle_other_deg1.53345262
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.70352525
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.16924.118782
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.859153557
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.99115110
X-RAY DIFFRACTIONr_chiral_restr0.0780.23063
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02122337
X-RAY DIFFRACTIONr_gen_planes_other0.0070.024157
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1720.21075
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2050.267
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1950.217
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.3043.35110148
X-RAY DIFFRACTIONr_mcbond_other2.3033.35110147
X-RAY DIFFRACTIONr_mcangle_it3.65.0212657
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.0413.789926
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A192160.09
12B192160.09
21A189390.09
22C189390.09
31A192160.08
32D192160.08
41A198310.06
42E198310.06
51A191950.09
52F191950.09
61A189670.09
62G189670.09
71A190580.09
72H190580.09
81B191480.09
82C191480.09
91B190550.1
92D190550.1
101B191850.09
102E191850.09
111B196360.08
112F196360.08
121B191490.09
122G191490.09
131B190640.1
132H190640.1
141C189320.1
142D189320.1
151C189150.09
152E189150.09
161C191010.09
162F191010.09
171C196500.06
172G196500.06
181C189220.09
182H189220.09
191D191860.08
192E191860.08
201D190390.1
202F190390.1
211D189430.1
212G189430.1
221D197360.06
222H197360.06
231E191420.09
232F191420.09
241E189400.09
242G189400.09
251E190210.09
252H190210.09
261F190940.09
262G190940.09
271F190230.1
272H190230.1
281G189420.09
282H189420.09
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.372 370 -
Rwork0.326 7161 -
obs--85.57 %

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