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

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Basic information

Entry
Database: PDB / ID: 5pzs
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-(3-chlorophenyl)sulfonyl-3-[6-[(3-chlorophenyl)sulfonylcarbamoylamino]hexyl]urea
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 / 2.368 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-(3-chlorophenyl)sulfonyl-3-[6-[(3-chlorophenyl)sulfonylcarbamoylamino]hexyl]urea
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)148,5416
Polyers147,4384
Non-polymers1,1032
Water11,241624
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)16420
ΔGint (kcal/M)-88
Surface area (Å2)44160
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)67.657, 83.267, 277.759
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-93Y / N,N'-(hexane-1,6-diyldicarbamoyl)bis(3-chlorobenzene-1-sulfonamide)


Mass: 551.464 Da / Num. of mol.: 2 / Formula: C20H24Cl2N4O6S2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 624 / 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: 55.12 %
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: Mar 17, 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: 2.368 Å / D resolution low: 29.888 Å / Number obs: 62129 / Percent possible obs: 95.71

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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: 0.3 / Cross valid method: THROUGHOUT / Sigma F: 1.38 / Overall phase error: 22.28 / 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: 95.38 Å2 / B iso mean: 29.0509 Å2 / B iso min: 4.91 Å2
Least-squares processR factor R free: 0.2325 / R factor R work: 0.1741 / R factor obs: 0.1771 / Highest resolution: 2.368 Å / Lowest resolution: 29.888 Å / Number reflection R free: 3138 / Number reflection R work: 58991 / Number reflection obs: 62129 / Percent reflection R free: 5.05 / Percent reflection obs: 95.71
Refine hist #finalHighest resolution: 2.368 Å / Lowest resolution: 29.888 Å / B iso mean ligand: 35.05 / B iso mean solvent: 34.87 / Number residues total: 1271
Number of atoms included #finalProtein: 9729 / Nucleic acid: 0 / Ligand: 68 / Solvent: 624 / Total: 10421
Refine LS restraints
Refine IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0079971
X-RAY DIFFRACTIONf_angle_d0.93213468
X-RAY DIFFRACTIONf_chiral_restr0.0561528
X-RAY DIFFRACTIONf_plane_restr0.0061719
X-RAY DIFFRACTIONf_dihedral_angle_d12.6486072
Refine LS restraints ncs

Ens ID: 1 / Number: 6095 / Refine ID: X-RAY DIFFRACTION / Rms: 9.706 / 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: 22

Highest resolutionR factor R freeR factor R workLowest resolutionNumber reflection R freeNumber reflection R workNumber reflection allPercent reflection obs
2.36850.28010.20062.4055701334140448.0000
2.40550.30930.19552.44491232277240082.0000
2.44490.26020.18482.48701222405252787.0000
2.48700.26980.19202.53221422620276295.0000
2.53220.28470.19852.58091292671280096.0000
2.58090.25490.19392.63361632664282798.0000
2.63360.28490.19572.69081482799294799.0000
2.69080.29460.19152.75331392719285899.0000
2.75330.27540.18432.822113827922930100.0000
2.82210.25300.18232.898415827592917100.0000
2.89840.25810.18702.983614627792925100.0000
2.98360.27820.19513.079814627942940100.0000
3.07980.25820.18333.189815827562914100.0000
3.18980.25140.17773.317313227992931100.0000
3.31730.21580.17273.468114728142961100.0000
3.46810.22890.16743.650614927842933100.0000
3.65060.23310.17253.878914728102957100.0000
3.87890.19480.15424.177713928532992100.0000
4.17770.17750.14484.596716028112971100.0000
4.59670.19840.14625.258715028653015100.0000
5.25870.20910.18196.613616028863046100.0000
6.61360.20790.177829.89081723000317299.0000
Refine TLS

Method: refined / Refine ID: X-RAY DIFFRACTION

IDL11L12L13L22L23L33S11S12S13S21S22S23S31S32S33T11T12T13T22T23T33Origin xOrigin yOrigin z
10.0527-0.00760.0577-0.00230.10230.11560.00640.0840-0.00050.01150.06700.0429-0.1458-0.07630.02730.14220.00220.02540.1003-0.00940.107117.240441.522121.0406
20.03640.00150.01860.0239-0.01570.0428-0.10250.1591-0.0007-0.07260.07590.13590.08420.0315-0.00500.11980.03770.03730.1146-0.02470.104816.445641.49478.5250
30.1011-0.03080.02460.1523-0.04050.07650.01130.07870.08890.0096-0.0109-0.0774-0.10470.0144-0.00380.1195-0.01770.00390.14600.00260.114734.626044.307311.2503
40.1330-0.06620.07650.1576-0.00570.09820.20420.2825-0.0465-0.1419-0.0372-0.15460.02520.14520.11200.0868-0.14810.03880.15530.03240.106836.847745.39553.1570
5-0.0470-0.0049-0.04170.0250-0.05780.0787-0.05630.0138-0.10860.04460.0235-0.0019-0.03040.0558-0.00270.19370.00910.02540.1155-0.01280.186231.825619.607535.8082
60.0143-0.03200.01060.0112-0.02630.0012-0.0600-0.0164-0.06850.03730.09560.1035-0.04880.16520.00000.15430.01170.02130.1572-0.01500.148045.753616.704539.6459
70.10490.05920.09820.11780.12410.11990.06220.14180.00520.14390.0151-0.0988-0.03450.07910.02520.1285-0.00920.00720.1511-0.01830.118046.587216.411532.6318
80.2197-0.13720.07620.1927-0.10250.14250.04140.0654-0.08380.0093-0.04150.06190.00190.19660.06520.0729-0.02520.01440.1647-0.04120.077041.311219.565814.3324
90.0658-0.02910.02210.0503-0.04140.0598-0.10230.0224-0.04800.0244-0.01700.0074-0.17220.1457-0.11580.01430.09270.00730.1850-0.10650.155250.711013.242416.8699
100.1080-0.05170.01880.0787-0.02260.0309-0.0447-0.00050.0241-0.00470.0461-0.0151-0.14060.06150.00050.1975-0.01030.02490.10010.00030.120815.906748.216141.7164
110.06680.03980.03700.1456-0.16400.1379-0.01300.02380.1903-0.05680.05570.1035-0.0505-0.07180.04550.14150.03700.00720.0985-0.00120.1046-1.535644.533546.9299
120.0869-0.04840.08440.1506-0.11330.22100.0097-0.13390.03780.07650.15030.1039-0.0369-0.11580.23580.14220.06720.02060.1247-0.04080.0974-4.851748.040853.7114
130.14390.0167-0.03960.0759-0.03670.16340.01490.0353-0.0735-0.0126-0.03600.01160.1230-0.0136-0.12080.08750.03220.00740.0573-0.01220.105212.177512.129037.0601
140.16570.0028-0.17550.1982-0.03400.19890.0027-0.0327-0.06180.04640.0112-0.02820.0626-0.00900.01610.1368-0.0089-0.00600.13060.03050.12412.651616.377355.4137
Refine TLS group

Refine ID: X-RAY DIFFRACTION

IDBeg auth asym IDBeg auth seq IDEnd auth asym IDEnd auth seq IDRefine TLS IDSelection details
1A9A881chain 'A' and (resid 9 through 88 )
2A89A1312chain 'A' and (resid 89 through 131 )
3A132A2473chain 'A' and (resid 132 through 247 )
4A248A3354chain 'A' and (resid 248 through 335 )
5B9B885chain 'B' and (resid 9 through 88 )
6B89B1226chain 'B' and (resid 89 through 122 )
7B123B1557chain 'B' and (resid 123 through 155 )
8B156B2748chain 'B' and (resid 156 through 274 )
9B275B3359chain 'B' and (resid 275 through 335 )
10C9C13110chain 'C' and (resid 9 through 131 )
11C132C24711chain 'C' and (resid 132 through 247 )
12C248C33512chain 'C' and (resid 248 through 335 )
13D9D12213chain 'D' and (resid 9 through 122 )
14D123D33514chain 'D' and (resid 123 through 335 )

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