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- PDB-7wvb: Human Fructose-1,6-bisphosphatase 1 mutant R50A in APO R-state -

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Basic information

Entry
Database: PDB / ID: 7wvb
TitleHuman Fructose-1,6-bisphosphatase 1 mutant R50A 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 / Resolution: 2.09 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 mutant R50A in APO R-state
Authors: Chen, Y. / Zhang, J. / Li, C. / Cao, Y.
History
DepositionFeb 10, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 15, 2023Provider: 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

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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


Theoretical massNumber of molelcules
Total (without water)147,2054
Polymers147,2054
Non-polymers00
Water5,062281
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8330 Å2
ΔGint-48 kcal/mol
Surface area44610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.182, 175.131, 81.607
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221

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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: 36801.316 Da / Num. of mol.: 4 / Mutation: R50A
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 281 / 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: 2.48 Å3/Da / Density % sol: 50.41 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M BIS-Tris(pH 6.5), 20% PEGMME 5000, 2.5% sucrose

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Data collection

DiffractionMean temperature: 77.2 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Jan 3, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.09→50 Å / Num. obs: 86259 / % possible obs: 99.3 % / Redundancy: 12.3 % / Biso Wilson estimate: 25.39 Å2 / Rmerge(I) obs: 0.173 / Rpim(I) all: 0.051 / Rrim(I) all: 0.181 / Χ2: 0.789 / Net I/σ(I): 4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.1-2.1410.20.95541590.7910.3061.0050.46197.1
2.14-2.1811.10.8442380.8490.2550.8790.46798.3
2.18-2.2211.40.81942270.8640.2480.8580.47298.6
2.22-2.2611.80.77842310.8730.2340.8140.48298.7
2.26-2.3112.10.70942340.8850.2110.7420.50198.9
2.31-2.3712.20.63742300.930.190.6660.51198.9
2.37-2.4211.70.54542870.9270.1670.5710.5298.9
2.42-2.4912.60.50842630.9560.1490.530.53499.2
2.49-2.5612.50.41942940.9740.1230.4370.55599.2
2.56-2.6512.20.35542640.9790.1060.3710.57399.5
2.65-2.7413.10.2943050.9840.0830.3020.61599.7
2.74-2.8513.10.23543180.9910.0670.2450.6599.5
2.85-2.98130.243100.990.0570.2080.72199.8
2.98-3.1412.50.1743270.9920.050.1770.79299.7
3.14-3.3313.30.13843250.9950.0390.1430.91999.7
3.33-3.5912.90.11443690.9950.0330.1191.11199.9
3.59-3.9513.60.09943750.9960.0280.1031.31599.7
3.95-4.5212.80.08743980.9970.0250.0911.49999.9
4.52-5.712.90.0844550.9970.0230.0831.43699.9
5.7-5011.80.0746500.9980.0210.0731.26599.9

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Processing

Software
NameVersionClassification
PHENIX1.20_4459refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
PHENIXmodel building
HKL-2000data reduction
PHENIX1.20_4459phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7cvh

7cvh


Resolution: 2.09→33.44 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2331 2000 2.34 %RANDOM
Rwork0.1948 83501 --
obs0.1957 85501 98.06 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 78.43 Å2 / Biso mean: 29.2749 Å2 / Biso min: 10.76 Å2
Refinement stepCycle: final / Resolution: 2.09→33.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8959 0 0 281 9240
Biso mean---29.64 -
Num. residues----1165
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.09-2.140.28991300.23085422555290
2.14-2.20.27741390.2155803594297
2.2-2.270.25231420.21525911605397
2.27-2.340.29871400.20455883602398
2.34-2.420.22231410.20325905604698
2.42-2.520.24441420.20795928607098
2.52-2.630.28781440.20545989613399
2.63-2.770.22661430.1995970611399
2.77-2.950.22841440.21176018616299
2.95-3.170.29811450.21156054619999
3.17-3.490.23161450.260746219100
3.49-40.22781470.180461066253100
4-5.030.17391480.163561696317100
5.04-33.440.21371500.18816269641997

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