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- PDB-7cwe: Human Fructose-1,6-bisphosphatase 1 in APO R-state -

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Basic information

Entry
Database: PDB / ID: 7cwe
TitleHuman Fructose-1,6-bisphosphatase 1 in APO R-state
ComponentsFructose-1,6-bisphosphatase 1
KeywordsHYDROLASE / APO-enzyme / Gluconeogenesis
Function / homology
Function and homology information


cellular response to raffinose / sucrose biosynthetic process / cellular hypotonic salinity response / cellular response to phorbol 13-acetate 12-myristate / fructose-bisphosphatase / fructose 1,6-bisphosphate 1-phosphatase activity / cellular response to magnesium ion / negative regulation of Ras protein signal transduction / fructose 6-phosphate metabolic process / Gluconeogenesis ...cellular response to raffinose / sucrose biosynthetic process / cellular hypotonic salinity response / cellular response to phorbol 13-acetate 12-myristate / fructose-bisphosphatase / fructose 1,6-bisphosphate 1-phosphatase activity / cellular response to magnesium ion / negative regulation of Ras protein signal transduction / fructose 6-phosphate metabolic process / Gluconeogenesis / fructose metabolic process / monosaccharide binding / negative regulation of glycolytic process / fructose 1,6-bisphosphate metabolic process / cellular hyperosmotic salinity response / regulation of gluconeogenesis / AMP binding / dephosphorylation / cellular response to cAMP / response to nutrient levels / gluconeogenesis / negative regulation of cell growth / cellular response to insulin stimulus / cellular response to xenobiotic stimulus / RNA polymerase II-specific DNA-binding transcription factor binding / negative regulation of transcription by RNA polymerase II / extracellular exosome / identical protein binding / nucleus / metal ion binding / cytoplasm / cytosol
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
Similarity search - Domain/homology
Fructose-1,6-bisphosphatase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3 Å
AuthorsChen, Y. / Zhang, J. / Li, C. / Cao, Y.
Funding support China, 3items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2018YFC1004704 China
National Natural Science Foundation of China (NSFC)31670849 China
National Natural Science Foundation of China (NSFC)U1632132 China
CitationJournal: To Be Published
Title: Human Fructose-1,6-bisphosphatase 1 in APO R-state
Authors: Zhang, J. / Chen, Y. / Li, C. / Cao, Y.
History
DepositionAug 28, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 8, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,8234
Polymers73,7752
Non-polymers492
Water00
1
A: Fructose-1,6-bisphosphatase 1
B: Fructose-1,6-bisphosphatase 1
hetero molecules

A: Fructose-1,6-bisphosphatase 1
B: Fructose-1,6-bisphosphatase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,6478
Polymers147,5504
Non-polymers974
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_554y,x,-z-1/41
Buried area13600 Å2
ΔGint-121 kcal/mol
Surface area47420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.305, 125.305, 108.030
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number91
Space group name H-MP4122

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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: 36887.434 Da / Num. of mol.: 2
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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
Has ligand of interestN

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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: 2.88 Å3/Da / Density % sol: 57.32 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.05 M cadmium sulfate, 0.1 M HEPES, pH 7.5, 1 M sodium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: May 26, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 3→38.96 Å / Num. obs: 17241 / % possible obs: 96.98 % / Redundancy: 5.62 % / Biso Wilson estimate: 58.91 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.197 / Net I/σ(I): 8.22
Reflection shellResolution: 3→3.05 Å / Num. unique obs: 1627 / CC1/2: 0.492

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-2000data scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2VT5

2vt5


Resolution: 3→38.96 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 28.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2963 1725 10.01 %
Rwork0.2575 15516 -
obs0.2614 17241 96.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 162.35 Å2 / Biso mean: 54.0851 Å2 / Biso min: 24.06 Å2
Refinement stepCycle: final / Resolution: 3→38.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4830 0 2 0 4832
Biso mean--29.37 --
Num. residues----630
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3-3.090.42231400.33831262140298
3.09-3.190.35651450.29761301144699
3.19-3.30.28751430.27311286142999
3.3-3.430.31021430.25321283142699
3.43-3.590.30251440.26281295143998
3.59-3.780.29891410.22671272141397
3.78-4.020.26431420.23311283142597
4.02-4.320.22641430.21241285142896
4.33-4.760.22891430.19841290143397
4.76-5.450.25541470.22551314146197
5.45-6.850.30751450.30531303144895
6.86-38.960.37561490.31381342149192
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)
1-0.00070.0318-0.02110.02370.04220.03240.05120.1365-0.0676-0.21450.0579-0.14860.1934-0.033900.3554-0.0151-0.00340.21370.06960.4544-48.0771-19.3272-13.081
2-0.0355-0.1692-0.0421-0.0262-0.1102-0.00840.04220.1853-0.05790.09390.2002-0.0654-0.17060.1126-00.36460.03010.05890.3398-0.07840.4068-36.3679-9.34-4.9341
30.05520.06820.0399-0.00110.01730.0210.1478-0.130.08610.16420.0450.1502-0.0332-0.0414-00.22030.03350.12070.3256-0.00930.4319-49.2567-3.4707-1.8351
40.041-0.0741-0.05230.03160.0110.0213-0.25340.22370.09150.21230.10950.00490.04530.131700.41640.09860.0220.2497-0.10240.2837-46.8589-24.161211.8369
5-0.0169-0.0097-0.00690.0092-0.01820.01020.02490.0258-0.03870.11230.00810.1065-0.28180.012100.4969-0.0375-0.00830.44170.06520.358-43.2682-17.268314.2134
6-0.04830.0473-0.0146-0.0479-0.01260.0091-0.2598-0.11340.0123-0.13610.21870.0661-0.08040.022-00.2759-0.08040.0490.4197-0.08770.3838-50.7547-11.159313.88
70.00260.018-0.01130.0137-0.00820.01920.041-0.15510.1965-0.21580.20480.23150.02570.020900.54770.12370.0090.3818-0.0280.5216-40.4651-9.512-23.6741
80.033-0.139-0.0914-0.05160.09770.07140.13120.03670.2243-0.0427-0.0351-0.00750.05370.054400.29970.03490.01530.32520.00380.3428-47.8839-30.1081-29.1781
90.07130.0613-0.0811-0.1613-0.05470.12170.26050.1475-0.27720.47090.3124-0.53-0.2959-0.3321-00.30520.09510.26210.45240.16460.1218-42.2848-19.9181-33.242
100.04160.01570.0496-0.0424-0.01650.06540.25660.08650.0354-0.04310.005-0.1507-0.0798-0.1707-00.43790.11440.13230.50860.06020.4003-25.4125-30.6991-53.3955
110.0606-0.0515-0.0721-0.0101-0.0013-0.00980.00530.1663-0.1089-0.1098-0.0813-0.2392-0.0341-0.212700.52730.12780.08440.4773-0.03970.3023-39.7994-26.9045-47.2178
12-0.0024-0.0112-0.01180.017-0.00410.0094-0.0171-0.09850.220.0294-0.1203-0.1196-0.00910.062100.88820.08010.19310.40480.0790.3941-31.3497-22.8883-60.4361
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 8 through 50 )A8 - 50
2X-RAY DIFFRACTION2chain 'A' and (resid 51 through 141 )A51 - 141
3X-RAY DIFFRACTION3chain 'A' and (resid 142 through 168 )A142 - 168
4X-RAY DIFFRACTION4chain 'A' and (resid 169 through 248 )A169 - 248
5X-RAY DIFFRACTION5chain 'A' and (resid 249 through 275 )A249 - 275
6X-RAY DIFFRACTION6chain 'A' and (resid 276 through 337 )A276 - 337
7X-RAY DIFFRACTION7chain 'B' and (resid 8 through 29 )B8 - 29
8X-RAY DIFFRACTION8chain 'B' and (resid 30 through 141 )B30 - 141
9X-RAY DIFFRACTION9chain 'B' and (resid 142 through 201 )B142 - 201
10X-RAY DIFFRACTION10chain 'B' and (resid 202 through 248 )B202 - 248
11X-RAY DIFFRACTION11chain 'B' and (resid 249 through 321 )B249 - 321
12X-RAY DIFFRACTION12chain 'B' and (resid 322 through 337 )B322 - 337

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