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Basic information

Entry
Database: PDB / ID: 5ldz
TitleQuadruple space group ambiguity due to rotational and translational non-crystallographic symmetry in human liver fructose-1,6-bisphosphatase
ComponentsFructose-1,6-bisphosphatase 1Fructose 1,6-bisphosphatase
KeywordsHYDROLASE / PHOSPHORIC MONOESTER / ALLOSTERIC ENZYME / CARBOHYDRATE / METABOLISM / 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 / 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 / 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 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 / 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
Fructose-1,6-bisphosphatase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsRuf, A. / Tetaz, T. / Schott, B. / Joseph, C. / Rudolph, M.G.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2016
Title: Quadruple space-group ambiguity owing to rotational and translational noncrystallographic symmetry in human liver fructose-1,6-bisphosphatase.
Authors: Ruf, A. / Tetaz, T. / Schott, B. / Joseph, C. / Rudolph, M.G.
History
DepositionJun 29, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 26, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 9, 2016Group: Database references
Revision 1.2Apr 18, 2018Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)224,80547
Polymers221,3256
Non-polymers3,48141
Water8,791488
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)149,93432
Polymers147,5504
Non-polymers2,38528
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18910 Å2
ΔGint-544 kcal/mol
Surface area45940 Å2
MethodPISA
2
E: Fructose-1,6-bisphosphatase 1
F: Fructose-1,6-bisphosphatase 1
hetero molecules

E: Fructose-1,6-bisphosphatase 1
F: Fructose-1,6-bisphosphatase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,74230
Polymers147,5504
Non-polymers2,19226
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_556-y,-x,-z+3/21
Buried area18450 Å2
ΔGint-513 kcal/mol
Surface area46440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.519, 121.519, 316.580
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#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.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FBP1, FBP / Plasmid: PET / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P09467, fructose-bisphosphatase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Zn
#3: Chemical...
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 29 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 488 / 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: 2.83 Å3/Da / Density % sol: 56.6 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1 M Tris-HCl pH 8.5, 2 M (NH4)2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 23, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.2→39.8 Å / Num. obs: 121069 / % possible obs: 99.7 % / Redundancy: 7.5 % / Biso Wilson estimate: 37.3 Å2 / CC1/2: 0.997 / Rsym value: 0.132 / Net I/σ(I): 7
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 4.4 % / Rmerge(I) obs: 1.22 / Mean I/σ(I) obs: 1.1 / CC1/2: 0.807 / % possible all: 97.9

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PDB_EXTRACT3.2data extraction
BUSTERrefinement
DENZOdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: inhouse model

Resolution: 2.2→39.8 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.935 / SU R Cruickshank DPI: 0.227 / Cross valid method: FREE R-VALUE / σ(F): 0 / SU R Blow DPI: 0.229 / SU Rfree Blow DPI: 0.185 / SU Rfree Cruickshank DPI: 0.186
Details: there is a short contact between two sulfate ions in the structure. Since the protein buffer contained phosphate, a hydrogenphosphate is probably present at one of these positions, but ...Details: there is a short contact between two sulfate ions in the structure. Since the protein buffer contained phosphate, a hydrogenphosphate is probably present at one of these positions, but cannot be resolved from sulfate.
RfactorNum. reflection% reflectionSelection details
Rfree0.239 6073 5.03 %RANDOM
Rwork0.206 ---
obs0.208 120699 99.9 %-
Displacement parametersBiso max: 170.32 Å2 / Biso mean: 46.53 Å2 / Biso min: 15.35 Å2
Baniso -1Baniso -2Baniso -3
1--5.5079 Å20 Å20 Å2
2---5.5079 Å20 Å2
3---11.0158 Å2
Refine analyzeLuzzati coordinate error obs: 0.32 Å
Refinement stepCycle: final / Resolution: 2.2→39.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14351 0 157 488 14996
Biso mean--91.75 43.31 -
Num. residues----1872
LS refinement shellResolution: 2.2→2.26 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 421 4.77 %
Rwork0.271 8397 -
all-8818 -
obs--99.95 %
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)
10-0.7887-2.1955.82330.74066.97060.0089-0.10210.02970.0593-0.07640.1619-0.13590.03680.06750.21180.0427-0.0269-0.0286-0.1301-0.096223.980352.1504208.355
22.0046-2.1096-1.21620.59330.7111.0717-0.0172-0.0948-0.02570.0997-0.001-0.0970.03660.1370.0182-0.03680.0171-0.0332-0.0523-0.0423-0.137116.537439.2737203.892
33.7697-1.8364-0.52241.31790.79550.0066-0.0463-0.0335-0.33630.16790.02540.15880.2215-0.32750.02090.09180.0348-0.01780.00470.0025-0.05698.065432.6031199.204
42.4457-0.9671-0.34011.4093-0.24951.4692-0.00270.03780.1624-0.0702-0.0274-0.0242-0.0403-0.16440.03020.04060.0334-0.038-0.0156-0.0413-0.076711.011442.274193.987
50.6344-0.4117-0.38580.54040.94443.94180.1013-0.00390.09080.00820.0234-0.1099-0.08560.0299-0.12470.0180.022-0.017-0.10920.0211-0.105228.49941.4329180.306
61.2055-0.3172-1.08131.2362-0.22.7039-0.07680.12260.002-0.1285-0.0220.05930.0171-0.30190.09880.08160.0336-0.0329-0.0411-0.0129-0.092917.164143.38178.008
702.21271.51142.5512-0.59887.1139-0.0041-0.1472-0.040.0457-0.0794-0.08020.05440.02760.08360.22610.0386-0.021-0.04950.0874-0.057636.548910.6352208.381
83.005-0.60710.27580.9485-0.08991.1940.0176-0.00370.0449-0.0303-0.016-0.0606-0.1190.0337-0.0016-0.0116-0.0034-0.0098-0.05280.0027-0.13450.987224.5892198.472
90.8476-0.42890.75580.7805-0.32182.66330.02860.0273-0.1084-0.0314-0.00660.07460.1907-0.149-0.0220.03240.0131-0.0132-0.0849-0.024-0.063535.792120.1999183.902
100.9527-0.52290.92111.11640.30052.6823-0.03130.076-0.0264-0.1664-0.0253-0.01230.02860.16220.05660.06280.0393-0.0143-0.0673-0.0008-0.097943.018319.4232177.96
110.58020.02530.00310.97620.10632.22590.017-0.022-0.0609-0.2019-0.0068-0.1753-0.0410.3184-0.01020.03990.0430.0403-0.0621-0.0036-0.096944.036821.615216.101
121.425-1.2915-0.50733.49810.39162.51440.01640.0232-0.20590.0348-0.10150.35020.0865-0.34260.08510.0731-0.0179-0.01830.0053-0.0014-0.046332.73610.7672224.076
1301.3471-0.448902.23651.69880.0299-0.0488-0.17970.00770.1085-0.17870.2821-0.0401-0.13840.08690.0377-0.007-0.15320.0094-0.098744.85555.5102227.939
140.8144-0.368-0.31670.72570.52422.2078-0.0136-0.08870.02680.01080.0464-0.0562-0.09070.0595-0.03280.01510.0514-0.0097-0.0455-0.0028-0.08140.854725.6544238.359
150.994-0.46280.04911.13321.14132.5471-0.0241-0.1862-0.02770.0264-0.03530.02760.32140.06780.05940.01070.0513-0.00060.00250.0189-0.111641.558718.4295244.315
160-0.0019-0.34630.3227-0.37181.49160.00850.1040.1183-0.31780.03270.01010.0762-0.2478-0.04120.1140.0573-0.0817-0.04-0.0274-0.139815.634441.4372215.805
170.2266-0.2952-0.13653.0248-0.10551.3147-0.0492-0.02410.09050.08180.0147-0.0325-0.16580.06550.03450.08310.0367-0.0248-0.0611-0.0296-0.121623.935253.7773224.828
180.633-0.31190.17070.8336-0.67211.7839-0.0448-0.0723-0.0622-0.01970.08020.14990.0254-0.1279-0.03540.00730.0470.0013-0.0291-0.0171-0.055618.437637.1174238.106
191.1163-0.1146-0.14290.8248-1.54291.84540.008-0.1725-0.00250.1435-0.0840.0131-0.2816-0.0150.0760.02110.06130.00170.0078-0.0139-0.100817.671944.3249243.918
200.99340.19250.58570.6518-0.05231.9959-0.0009-0.0978-0.07280.1841-0.00870.1112-0.0445-0.34260.00960.00480.02230.05610.0049-0.0062-0.1246-45.411721.4818232.482
210.10140.7328-1.03782.2233-0.47391.88330.0096-0.1101-0.12960.0172-0.0776-0.37260.31820.32720.0680.02820.0220.0010.0593-0.0034-0.026-32.49839.1464225.895
220.70681.37540.0185.1608-0.53652.4510.00340.0574-0.1283-0.1311-0.00180.01970.11790.0209-0.00170.01020.06280.0001-0.0413-0.0219-0.1008-39.97749.9182221.697
230.6801-0.0405-0.57490.86-0.33122.0994-0.04880.0637-0.0127-0.08390.07820.0409-0.0097-0.0975-0.0295-0.0342-0.0096-0.02710.0109-0.0187-0.0933-42.207625.3253210.178
240.94420.6982-0.19491.1475-1.07292.4796-0.01760.1433-0.0719-0.1849-0.0599-0.10550.34570.00990.07740.0056-0.0011-0.01560.0241-0.0266-0.1067-42.923618.127204.441
251.3655-0.39880.386800.29731.93850.0207-0.12570.05890.16650.02170.01830.08590.2678-0.0424-0.00510.0378-0.03430.0239-0.0166-0.1181-16.938841.2588232.472
260.72810.8149-0.18013.54860.22121.5251-0.0292-0.02650.0782-0.13520.00550.1031-0.0526-0.18380.02370.02740.0498-0.00560.013-0.005-0.1109-25.161953.6175223.499
270.76850.44850.25090.55680.74751.8582-0.0550.0557-0.0319-0.02930.0742-0.11630.07420.1213-0.0192-0.00360.01430.0229-0.0124-0.0192-0.0654-19.794936.8089210.319
281.12260.6183-0.05890.24850.85292.4417-0.07770.14150.0086-0.1261-0.04770.0339-0.22250.02040.12530.0262-0.00070.02080.002-0.0076-0.094-18.94743.9336204.278
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|6 - A|29 }A6 - 29
2X-RAY DIFFRACTION2{ A|30 - A|50 }A30 - 50
3X-RAY DIFFRACTION3{ A|51 - A|107 }A51 - 107
4X-RAY DIFFRACTION4{ A|108 - A|180 }A108 - 180
5X-RAY DIFFRACTION5{ A|181 - A|248 }A181 - 248
6X-RAY DIFFRACTION6{ A|249 - A|336 }A249 - 336
7X-RAY DIFFRACTION7{ B|6 - B|29 }B6 - 29
8X-RAY DIFFRACTION8{ B|30 - B|149 }B30 - 149
9X-RAY DIFFRACTION9{ B|150 - B|248 }B150 - 248
10X-RAY DIFFRACTION10{ B|249 - B|337 }B249 - 337
11X-RAY DIFFRACTION11{ C|6 - C|50 }C6 - 50
12X-RAY DIFFRACTION12{ C|51 - C|132 }C51 - 132
13X-RAY DIFFRACTION13{ C|133 - C|149 }C133 - 149
14X-RAY DIFFRACTION14{ C|150 - C|248 }C150 - 248
15X-RAY DIFFRACTION15{ C|249 - C|337 }C249 - 337
16X-RAY DIFFRACTION16{ D|6 - D|50 }D6 - 50
17X-RAY DIFFRACTION17{ D|51 - D|149 }D51 - 149
18X-RAY DIFFRACTION18{ D|150 - D|248 }D150 - 248
19X-RAY DIFFRACTION19{ D|249 - D|336 }D249 - 336
20X-RAY DIFFRACTION20{ E|6 - E|50 }E6 - 50
21X-RAY DIFFRACTION21{ E|51 - E|107 }E51 - 107
22X-RAY DIFFRACTION22{ E|108 - E|149 }E108 - 149
23X-RAY DIFFRACTION23{ E|150 - E|248 }E150 - 248
24X-RAY DIFFRACTION24{ E|249 - E|336 }E249 - 336
25X-RAY DIFFRACTION25{ F|6 - F|50 }F6 - 50
26X-RAY DIFFRACTION26{ F|51 - F|149 }F51 - 149
27X-RAY DIFFRACTION27{ F|150 - F|248 }F150 - 248
28X-RAY DIFFRACTION28{ F|249 - F|337 }F249 - 337

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