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- PDB-7cvh: Human Fructose-1,6-bisphosphatase 1 in complex with geranylgerany... -

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Basic information

Entry
Database: PDB / ID: 7cvh
TitleHuman Fructose-1,6-bisphosphatase 1 in complex with geranylgeranyl diphosphate
ComponentsFructose-1,6-bisphosphatase 1Fructose 1,6-bisphosphatase
KeywordsHYDROLASE / gluconeogenesis / cholesterol synthesis / complex
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 / negative regulation of Ras protein signal transduction / fructose 1,6-bisphosphate metabolic process / cellular response to magnesium ion / fructose 6-phosphate metabolic process ...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 / negative regulation of Ras protein signal transduction / fructose 1,6-bisphosphate metabolic process / cellular response to magnesium ion / fructose 6-phosphate metabolic process / fructose metabolic process / Gluconeogenesis / monosaccharide binding / negative regulation of glycolytic 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 / metal ion binding / nucleus / cytosol / cytoplasm
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
ADENOSINE MONOPHOSPHATE / 1,6-di-O-phosphono-beta-D-fructofuranose / GERANYLGERANYL DIPHOSPHATE / 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, 4items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2018YFC1004704 China
Ministry of Science and Technology (MoST, China)2018YFC1004703 China
National Natural Science Foundation of China (NSFC)31670849 China
National Natural Science Foundation of China (NSFC)U1632132 China
CitationJournal: To Be Published
Title: The structural basis for GGPP activation on the enzymatic activities FBP1
Authors: Chen, Y. / Zhang, J. / Li, C. / Cao, Y.
History
DepositionAug 26, 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
C: Fructose-1,6-bisphosphatase 1
B: Fructose-1,6-bisphosphatase 1
D: Fructose-1,6-bisphosphatase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,94421
Polymers147,5504
Non-polymers3,39417
Water18,9881054
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23500 Å2
ΔGint-201 kcal/mol
Surface area42150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.392, 83.426, 277.355
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Sugars , 2 types, 8 molecules ACBD

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


Mass: 36887.434 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: Sugar
ChemComp-FBP / 1,6-di-O-phosphono-beta-D-fructofuranose / BETA-FRUCTOSE-1,6-DIPHOSPHATE / FRUCTOSE-1,6-BISPHOSPHATE / 1,6-di-O-phosphono-beta-D-fructose / 1,6-di-O-phosphono-D-fructose / 1,6-di-O-phosphono-fructose / Fructose 1,6-bisphosphate


Type: D-saccharide, beta linking / Mass: 340.116 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O12P2
IdentifierTypeProgram
b-D-Fruf1PO36PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 4 types, 1067 molecules

#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#5: Chemical ChemComp-GRG / GERANYLGERANYL DIPHOSPHATE / Geranylgeranyl pyrophosphate


Mass: 450.443 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H36O7P2 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1054 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.64 Å3/Da / Density % sol: 53.45 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 28% (v/v) polyethylene glycol 600, 0.1M HEPES

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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 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.09→50 Å / Num. obs: 89144 / % possible obs: 95.8 % / Redundancy: 3.7 % / Biso Wilson estimate: 17.17 Å2 / Rmerge(I) obs: 0.366 / Rpim(I) all: 0.187 / Rrim(I) all: 0.413 / Χ2: 0.942 / Net I/σ(I): 3.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.1-2.142.51.01942570.3520.6921.240.87493.5
2.14-2.182.51.02142890.3540.691.240.88192.9
2.18-2.222.81.04642280.3890.6581.2440.88593.3
2.22-2.263.11.08743530.4210.6341.2650.89193.6
2.26-2.313.31.09443590.5070.6121.260.92895.9
2.31-2.373.61.06243970.5850.5651.210.89895.5
2.37-2.423.81.06344230.5990.5491.2020.90896.2
2.42-2.493.91.12944590.6360.561.2660.89896.7
2.49-2.5641.07544970.6850.5231.2010.89697.3
2.56-2.654.10.96844240.6990.4711.0810.90596.5
2.65-2.743.90.7944690.7260.3990.8890.89396.3
2.74-2.853.90.63444190.8340.3210.7150.92495.8
2.85-2.984.20.53944790.8810.260.6020.94696.4
2.98-3.144.30.43545250.930.2030.4820.94897.5
3.14-3.334.20.31645610.9620.1490.3511.00897.9
3.33-3.594.20.22445300.9720.1070.2491.05796.8
3.59-3.953.90.16445370.980.0830.1851.07396.9
3.95-4.523.90.1245660.9730.0610.1350.99596.4
4.52-5.74.20.10146050.9920.0480.1130.97596.4
5.7-503.80.07847670.9970.040.0880.91395

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Processing

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

2vt5


Resolution: 2.09→41.25 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 20.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2183 2000 2.25 %
Rwork0.178 86983 -
obs0.1789 88983 95.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 92.4 Å2 / Biso mean: 20.2401 Å2 / Biso min: 5.66 Å2
Refinement stepCycle: final / Resolution: 2.09→41.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9779 0 238 1054 11071
Biso mean--19.27 29.57 -
Num. residues----1278
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 (%)
2.09-2.150.28231320.21715749588189
2.15-2.20.27721380.20535988612693
2.2-2.270.2671380.2016012615094
2.27-2.340.21761410.18726128626995
2.34-2.430.24351430.18316183632696
2.43-2.520.20941430.18976253639697
2.52-2.640.25261440.19676245638997
2.64-2.780.22651430.19316247639097
2.78-2.950.20631430.18436192633596
2.95-3.180.24841450.18326346649198
3.18-3.50.19871460.17356355650198
3.5-40.21131460.15666348649497
4-5.040.16731470.14276399654697
5.04-41.250.20541510.17926538668995
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)
10.00030-0.00010.00030.00010.00010.0010.00060.00210.00050.0012-0.00260.00030.002200.0573-0.01630.01260.06460.00470.082226.9701-9.5681-46.7012
20.0006-0.00020.00060.0002-0.00030.0001-0.0073-0.00450.01340.003-0.0109-0.00480.0008-0.008100.01180.0092-0.01330.00610.00530.023411.1897-22.2123-32.799
30.0015-0.0015-0.00130.00120.0003-0.00010.0022-0.0103-0.00190.00340.0060.0087-0.00610.004-00.03410.01680.00480.0005-0.00860.06696.053-7.4684-35.3037
40.002-0.0017-0.00040.00070.00060.0017-0.0141-0.00450.00150.0026-0.00790.002-0.0017-0.0057-00.02610.00730.004-0.0119-0.00130.04593.4569-9.9232-43.3375
50.0024-0.0010.00060.0018-0.00450.00360.02230.00430.0132-0.01630.0128-0.0151-0.0082-0.0006-00.017-0.0019-0.01190.03350.01910.02717.1392-21.3042-55.5408
60.00010.000200.0005-0.00010.00070.0044-0.0012-0.0003-0.0015-0.0014-0.0006-0.00090.0012-00.01350.0047-0.01130.0012-0.01680.0012-1.2107-30.9688-66.2366
7-0.0001-0.0002-00.00010.00010.0003-0.0017-0.0023-0.00170.0029-0.0072-0.00110.0032-0.007500.01320.0126-0.0140.0130.00680.021-1.8511-20.9915-56.0914
8-0.00060.00210.00050.0009-0.00120.00010.00430.00480.0043-0.00750.0008-0.00040.0022-0.002700.02730.0085-0.00930.00910.0435-0.0016-0.8544-12.1858-59.0641
90.0031-0.00150.00020.00570.00360.00040.0074-0.0118-0.00850.00220.0092-0.00550.02530.003800.0693-0.0015-0.0164-0.0848-0.0430.0214.7357-51.47-42.5091
10-0.00050.0019-0.00060.00220.0002-0.00070.00760.01010.001-0.00260.03520.02890.0359-0.0318-0-0.0753-0.1433-0.0912-0.0951-0.0737-0.0252-4.6003-44.9696-49.8011
110.0002-0.0001-0.00050.0004-0-0.0001-0.00030.00030.0023-00.00150.0001-0.0013-0.002600.0640.00860.00240.056-0.01660.102425.7823-5.2691-32.8229
120.00180.0001-0.00030.00020.0002-0.0011-0.00060.00420.0010.001-0.0017-0.002-0.00240.006400.0336-0.0025-0.00960.0401-0.01520.047431.9483-28.6726-36.1767
130.00110.0005-0.00110.00060.00050.00010.00260.0032-0.0011-0.00280.0012-0.00210.00190.0091-00.0223-0.01450.00610.0507-0.00940.060743.6751-19.0236-40.6745
140.00050-0.00110.00180.00150.00040.00510.00240.0155-0.0165-0.0046-0.010700.0116-00.0149-0.0171-0.0130.0466-0.02560.047642.2773-16.7244-29.6734
150.0008-0.0001-0.001-0.00030.00060.00160.0172-0.01060.00860.0104-0.0040.0143-0.0110.016-0-0.0187-0.0282-0.03280.0766-0.0568-0.003940.33-20.6214-10.4869
160.00090.00140.0003-0.0011-0.00020.001-0.0056-0.01540.003-0.005-0.0218-0.01320.00350.01230-0.0284-0.0729-0.04920.0948-0.0803-0.001549.118-16.2912-16.4795
17-0.0001-0.0005-0.00120.0015-0.00290.00210.0137-0.0211-0.0003-0.0056-0.00670.00740.0231-0.013300.0718-0.0052-0.0050.0544-0.00020.031815.2869-42.7307-16.3734
180.00160.00150.00410.0016-0.00760.0034-0.0066-0.035-0.01970.0096-0.00780.00550.03050.0194-00.03040.07-0.03770.04830.03430.016633.7437-43.1751-10.8901
190.0013-0.00120.00150.0009-0.0020.00070.0162-0.0099-0.0008-0.0001-0.011-0.0080.010.01100.08890.0975-0.05240.10.04550.02736.5699-45.5222-2.782
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 10 through 29 )A10 - 29
2X-RAY DIFFRACTION2chain 'A' and (resid 30 through 73 )A30 - 73
3X-RAY DIFFRACTION3chain 'A' and (resid 74 through 119 )A74 - 119
4X-RAY DIFFRACTION4chain 'A' and (resid 120 through 156 )A120 - 156
5X-RAY DIFFRACTION5chain 'A' and (resid 157 through 232 )A157 - 232
6X-RAY DIFFRACTION6chain 'A' and (resid 233 through 248 )A233 - 248
7X-RAY DIFFRACTION7chain 'A' and (resid 249 through 275 )A249 - 275
8X-RAY DIFFRACTION8chain 'A' and (resid 276 through 336 )A276 - 336
9X-RAY DIFFRACTION9chain 'C' and (resid 10 through 156 )C10 - 156
10X-RAY DIFFRACTION10chain 'C' and (resid 157 through 336 )C157 - 336
11X-RAY DIFFRACTION11chain 'B' and (resid 10 through 29 )B10 - 29
12X-RAY DIFFRACTION12chain 'B' and (resid 30 through 73 )B30 - 73
13X-RAY DIFFRACTION13chain 'B' and (resid 74 through 119 )B74 - 119
14X-RAY DIFFRACTION14chain 'B' and (resid 120 through 180 )B120 - 180
15X-RAY DIFFRACTION15chain 'B' and (resid 181 through 248 )B181 - 248
16X-RAY DIFFRACTION16chain 'B' and (resid 249 through 336 )B249 - 336
17X-RAY DIFFRACTION17chain 'D' and (resid 10 through 119 )D10 - 119
18X-RAY DIFFRACTION18chain 'D' and (resid 120 through 248 )D120 - 248
19X-RAY DIFFRACTION19chain 'D' and (resid 249 through 336 )D249 - 336

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