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- PDB-5pzv: Human liver fructose-1,6-bisphosphatase 1 (fructose 1,6-bisphosph... -

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Basic information

Entry
Database: PDB / ID: 5pzv
TitleHuman liver fructose-1,6-bisphosphatase 1 (fructose 1,6-bisphosphate 1-phosphatase, E.C.3.1.3.11) complexed with the allosteric inhibitor 1-(4-bromopyridin-2-yl)-3-(4-chlorophenyl)sulfonylurea
ComponentsFructose-1,6-bisphosphatase 1Fructose 1,6-bisphosphatase
KeywordsHYDROLASE/HYDROLASE inhibitor / D3R docking / HYDROLASE-HYDROLASE inhibitor complex
Function / homologyFructose-1,6-bisphosphatase class 1 / Fructose-1,6-bisphosphatase, active site / Fructose-1,6-bisphosphatase / Fructose-1-6-bisphosphatase class I, N-terminal / Fructose-1-6-bisphosphatase, N-terminal domain / Fructose-1-6-bisphosphatase active site. / fructose 1,6-bisphosphate 1-phosphatase activity / carbohydrate metabolic process / Fructose-1,6-bisphosphatase 1
Function and homology information
Specimen sourceHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / 2 Å resolution
Model detailsFor D3R project
AuthorsRuf, A. / Joseph, C. / Alker, A. / Banner, D. / Tetaz, T. / Benz, J. / Kuhn, B. / Rudolph, M.G. / Yang, H. / Shao, C. / Burley, S.K.
CitationJournal: To be published
Title: Human liver fructose-1,6-bisphosphatase 1 (fructose 1,6-bisphosphate 1-phosphatase, E.C.3.1.3.11) complexed with the allosteric inhibitor 1-(4-bromopyridin-2-yl)-3-(4-chlorophenyl)sulfonylurea
Authors: Ruf, A. / Joseph, C. / Alker, A. / Banner, D. / Tetaz, T. / Benz, J. / Kuhn, B. / Rudolph, M.G.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Apr 11, 2017 / Release: Jan 9, 2019
RevisionDateData content typeGroupCategoryItemProviderType
1.0Jan 9, 2019Structure modelrepositoryInitial release
1.1Jan 16, 2019Structure modelData collectiondiffrn_radiation_diffrn_radiation.pdbx_diffrn_protocol
1.2Feb 6, 2019Structure modelData collection / Database references / Structure summaryaudit_author / citation_author_audit_author.name / _citation_author.name

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,0008
Polyers147,4384
Non-polymers1,5634
Water18,0511002
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)15960
ΔGint (kcal/M)-75
Surface area (Å2)43750
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)67.618, 83.409, 277.065
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP 21 21 21

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Components

#1: Protein/peptide
Fructose-1,6-bisphosphatase 1 / Fructose 1,6-bisphosphatase / Growth-inhibiting protein 17 / cDNA FLJ75786 / highly similar to Homo sapiens fructose-1 / 6-bisphosphatase 1 (FBP1) / mRNA


Mass: 36859.418 Da / Num. of mol.: 4 / Source: (gene. exp.) Homo sapiens (human) / Gene: FBP1, hCG_1640493 / Production host: Escherichia coli (E. coli) / References: UniProt: Q2TU34, fructose-bisphosphatase
#2: Chemical
ChemComp-94G / N-[(4-bromopyridin-2-yl)carbamoyl]-4-chlorobenzene-1-sulfonamide


Mass: 390.640 Da / Num. of mol.: 4 / Formula: C12H9BrClN3O3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1002 / Formula: H2O / Water

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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: 2.74 / Density percent sol: 55.06 %
Crystal growTemp: 300 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1M HEPES pH 7.0, 0.1M AMMONIUM ACETATE, 12% PEG 3350

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Data collection

DiffractionMean temperature: 100 kelvins
SourceSource: SYNCHROTRON / Type: SLS BEAMLINE X10SA / Synchrotron site: SLS / Beamline: X10SA / Wavelength: 0.987
DetectorType: MAR CCD 165 mm / Detector: CCD / Collection date: Apr 13, 2006
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionD resolution high: 2 Å / D resolution low: 29.672 Å / Number obs: 100175 / Percent possible obs: 93.75

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationContact authorContact author emailDateLanguageLocationType
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.23data extractionPDBdeposit[at]deposit.rcsb.orgDec. 13, 2016C++http://sw-tools.pdb.org/apps/PDB_EXTRACT/package
RefineMethod to determine structure: MOLECULAR REPLACEMENT / Overall SU ML: 0.27 / Cross valid method: THROUGHOUT / Sigma F: 1.36 / Overall phase error: 22.23 / Stereochemistry target values: ML
Solvent computationSolvent shrinkage radii: 0.9 Å / Solvent vdw probe radii: 1.11 Å / Solvent model details: FLAT BULK SOLVENT MODEL
Displacement parametersB iso max: 108.9 Å2 / B iso mean: 29.6444 Å2 / B iso min: 5.02 Å2
Least-squares processR factor R free: 0.2388 / R factor R work: 0.1906 / R factor obs: 0.193 / Highest resolution: 2 Å / Lowest resolution: 29.672 Å / Number reflection R free: 5009 / Number reflection R work: 95166 / Number reflection obs: 100175 / Percent reflection R free: 5 / Percent reflection obs: 93.75
Refine hist #finalHighest resolution: 2 Å / Lowest resolution: 29.672 Å / B iso mean ligand: 56.99 / B iso mean solvent: 37.29 / Number residues total: 1271
Number of atoms included #finalProtein: 9729 / Nucleic acid: 0 / Ligand: 84 / Solvent: 1002 / Total: 10815
Refine LS restraints
Refine IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0079989
X-RAY DIFFRACTIONf_angle_d0.91013496
X-RAY DIFFRACTIONf_chiral_restr0.0571528
X-RAY DIFFRACTIONf_plane_restr0.0061723
X-RAY DIFFRACTIONf_dihedral_angle_d10.4496062
Refine LS restraints ncs

Ens ID: 1 / Number: 6090 / Refine ID: X-RAY DIFFRACTION / Rms: 9.362 / Type: TORSIONAL

Dom IDAuth asym ID
1A
2B
3C
4D
Refine LS shell

Refine ID: X-RAY DIFFRACTION / R factor R free error: 0 / Total number of bins used: 30

Highest resolutionR factor R freeR factor R workLowest resolutionNumber reflection R freeNumber reflection R workNumber reflection allPercent reflection obs
2.00000.34330.27052.02271742899307387.0000
2.02270.32510.25222.04651572851300885.0000
2.04650.31490.25532.07151432896303987.0000
2.07150.31840.24902.09771532917307087.0000
2.09770.33600.24502.12531852903308888.0000
2.12530.30220.22952.15441492957310688.0000
2.15440.25610.22472.18521412983312488.0000
2.18520.32300.22512.21781342984311889.0000
2.21780.29630.21982.25241782942312088.0000
2.25240.26020.21242.28931552977313290.0000
2.28930.23930.20452.32881533032318589.0000
2.32880.29140.20152.37111473032317991.0000
2.37110.25540.19402.41671803013319390.0000
2.41670.27090.19812.46601563080323692.0000
2.46600.25070.20272.51961573111326892.0000
2.51960.25030.20382.57821803102328294.0000
2.57820.25900.20252.64261613204336595.0000
2.64260.24120.20222.71401593235339496.0000
2.71400.24510.19502.79381653310347598.0000
2.79380.25490.19292.88391983320351899.0000
2.88390.24190.19582.986917933853564100.0000
2.98690.24080.19823.106416533773542100.0000
3.10640.22800.19063.247615934313590100.0000
3.24760.23580.18043.418620233383540100.0000
3.41860.22200.16993.632418434193603100.0000
3.63240.22060.16683.912317734263603100.0000
3.91230.18150.16264.304918234443626100.0000
4.30490.17370.14664.925419134363627100.0000
4.92540.22110.17736.196217435143688100.0000
6.19620.22480.190229.67501713648381999.0000
Refine TLS

Method: refined / Refine ID: X-RAY DIFFRACTION

IDL11L12L13L22L23L33S11S12S13S21S22S23S31S32S33T11T12T13T22T23T33Origin xOrigin yOrigin z
10.04270.00980.00430.0170-0.03120.0420-0.08140.0802-0.00940.03110.13760.0137-0.0409-0.02570.00130.17450.01190.03570.15380.00960.133217.067641.873216.0126
20.03430.0154-0.02940.0633-0.05850.0596-0.03880.11970.0775-0.00520.0072-0.0204-0.12540.0709-0.06360.1160-0.06360.04160.17960.01250.109334.719944.622610.9063
30.0142-0.0173-0.00400.00320.00100.00640.04760.0638-0.0004-0.0546-0.0020-0.0998-0.07320.11760.00000.2160-0.05870.06260.25840.00160.161736.939345.58252.8340
40.0355-0.02420.01610.01790.00830.01320.0034-0.0290-0.04030.08450.03360.0376-0.01550.06000.00190.09620.00760.01300.1302-0.03180.146036.562319.252937.2165
50.0588-0.0293-0.02650.0562-0.00390.00870.09840.1318-0.13690.00710.03620.0328-0.05880.15740.17370.1236-0.00340.08040.2384-0.11230.084341.613918.521818.9496
60.01160.01780.00820.03130.00250.0334-0.06830.0649-0.0968-0.0175-0.0604-0.0403-0.01780.1191-0.10660.11380.08750.08120.3023-0.16270.043049.660916.330816.4007
70.0247-0.01290.00950.05900.03150.0175-0.0070-0.01390.0387-0.10090.0356-0.0522-0.0396-0.0056-0.01320.12520.00430.04020.0574-0.02230.089916.184648.863441.5068
80.0402-0.0304-0.00880.0624-0.02690.04550.0027-0.02260.05770.0218-0.00460.0860-0.0026-0.0642-0.02390.11290.03400.05000.0916-0.01360.1169-2.746646.867949.6561
90.03000.0264-0.01420.0278-0.03580.0259-0.01580.0578-0.1076-0.05150.0455-0.01930.0571-0.01520.00750.12470.01570.01460.0768-0.02010.130812.226512.734637.0258
100.15140.0647-0.06430.0739-0.02410.07580.0491-0.0214-0.07700.1085-0.0276-0.01860.0422-0.00090.07300.1156-0.00640.05610.06730.01590.05982.597417.111455.3823
Refine TLS group

Refine ID: X-RAY DIFFRACTION

IDBeg auth asym IDBeg auth seq IDEnd auth asym IDEnd auth seq IDRefine TLS IDSelection details
1A9A1311chain 'A' and (resid 9 through 131 )
2A132A2472chain 'A' and (resid 132 through 247 )
3A248A3353chain 'A' and (resid 248 through 335 )
4B9B1224chain 'B' and (resid 9 through 122 )
5B123B2475chain 'B' and (resid 123 through 247 )
6B248B3356chain 'B' and (resid 248 through 335 )
7C9C1317chain 'C' and (resid 9 through 131 )
8C132C3358chain 'C' and (resid 132 through 335 )
9D9D1229chain 'D' and (resid 9 through 122 )
10D123D33510chain 'D' and (resid 123 through 335 )

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