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- PDB-5oez: Crystal structure of Leishmania major fructose-1,6-bisphosphatase... -

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Basic information

Entry
Database: PDB / ID: 5oez
TitleCrystal structure of Leishmania major fructose-1,6-bisphosphatase in apo form.
ComponentsFBP protein
KeywordsHYDROLASE / Allostery / Gluconeogenesis
Function / homology
Function and homology information


fructose-bisphosphatase / fructose 1,6-bisphosphate 1-phosphatase activity / glycosome / fructose 1,6-bisphosphate metabolic process / fructose metabolic process / fructose 6-phosphate metabolic process / gluconeogenesis / nucleotide binding / metal ion binding / cytoplasm / cytosol
Similarity search - Function
Fructose-1,6-bisphosphatase / Fructose-1,6-bisphosphatase, active site / Fructose-1-6-bisphosphatase active site. / Fructose-1,6-bisphosphatase class 1 / Fructose-1-6-bisphosphatase class I, N-terminal / Fructose-1-6-bisphosphatase class 1, C-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 active site. / Fructose-1,6-bisphosphatase class 1 / Fructose-1-6-bisphosphatase class I, N-terminal / Fructose-1-6-bisphosphatase class 1, C-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-bisphosphatase
Similarity search - Component
Biological speciesLeishmania major (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.41 Å
AuthorsYuan, M. / Vasquez-Valdivieso, M.G. / McNae, I.W. / Michels, P.A.M. / Fothergill-Gilmore, L.A. / Walkinshaw, M.D.
CitationJournal: J. Mol. Biol. / Year: 2017
Title: Structures of Leishmania Fructose-1,6-Bisphosphatase Reveal Species-Specific Differences in the Mechanism of Allosteric Inhibition.
Authors: Yuan, M. / Vasquez-Valdivieso, M.G. / McNae, I.W. / Michels, P.A.M. / Fothergill-Gilmore, L.A. / Walkinshaw, M.D.
History
DepositionJul 10, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 20, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FBP protein
B: FBP protein
C: FBP protein
D: FBP protein


Theoretical massNumber of molelcules
Total (without water)155,4904
Polymers155,4904
Non-polymers00
Water2,252125
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12920 Å2
ΔGint-42 kcal/mol
Surface area44230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.260, 162.560, 170.130
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: THR / Beg label comp-ID: THR / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ARGARGAA8 - 3378 - 337
21ARGARGBB8 - 3378 - 337
12ASPASPAA8 - 3368 - 336
22ASPASPCC8 - 3368 - 336
13ARGARGAA8 - 3378 - 337
23ARGARGDD8 - 3378 - 337
14ASPASPBB8 - 3368 - 336
24ASPASPCC8 - 3368 - 336
15ARGARGBB8 - 3378 - 337
25ARGARGDD8 - 3378 - 337
16ASPASPCC8 - 3368 - 336
26ASPASPDD8 - 3368 - 336

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
FBP protein


Mass: 38872.383 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania major (eukaryote) / Gene: FBP, LMJF_04_1160
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: O97193, fructose-bisphosphatase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / 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: 2.46 Å3/Da / Density % sol: 49.94 %
Crystal growTemperature: 290.15 K / Method: vapor diffusion / pH: 5
Details: 20% w/v PEG 3,350, 0.05 M citric acid, 0.05 M Bis-Tris propane

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: May 13, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.41→58.77 Å / Num. obs: 59755 / % possible obs: 99.4 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.094 / Net I/σ(I): 9.2
Reflection shellResolution: 2.41→2.496 Å / Mean I/σ(I) obs: 2.9 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5FBP

5fbp


Resolution: 2.41→58.77 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.941 / SU B: 17.519 / SU ML: 0.186 / Cross valid method: THROUGHOUT / ESU R: 0.348 / ESU R Free: 0.231 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22536 3019 5.1 %RANDOM
Rwork0.18699 ---
obs0.18886 56736 99.23 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å
Displacement parametersBiso mean: 66.097 Å2
Baniso -1Baniso -2Baniso -3
1--0.61 Å2-0 Å2-0 Å2
2--0.26 Å2-0 Å2
3---0.34 Å2
Refinement stepCycle: 1 / Resolution: 2.41→58.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9747 0 0 125 9872
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0199952
X-RAY DIFFRACTIONr_bond_other_d0.0070.029551
X-RAY DIFFRACTIONr_angle_refined_deg1.4951.95813458
X-RAY DIFFRACTIONr_angle_other_deg1.473321948
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.08151240
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.20423.349430
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.366151737
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.381573
X-RAY DIFFRACTIONr_chiral_restr0.0870.21500
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02111196
X-RAY DIFFRACTIONr_gen_planes_other0.0050.022293
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.5793.6584978
X-RAY DIFFRACTIONr_mcbond_other5.583.6584977
X-RAY DIFFRACTIONr_mcangle_it7.6485.4816209
X-RAY DIFFRACTIONr_mcangle_other7.6475.4826210
X-RAY DIFFRACTIONr_scbond_it8.0824.4194974
X-RAY DIFFRACTIONr_scbond_other8.0814.424975
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other11.0036.3277249
X-RAY DIFFRACTIONr_long_range_B_refined13.45429.93710852
X-RAY DIFFRACTIONr_long_range_B_other13.45829.92410843
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A363840.11
12B363840.11
21A364360.1
22C364360.1
31A359680.12
32D359680.12
41B362600.1
42C362600.1
51B354580.12
52D354580.12
61C355820.12
62D355820.12
LS refinement shellResolution: 2.41→2.473 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 224 -
Rwork0.267 4115 -
obs--99.68 %
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)
11.25540.48850.31553.28090.77661.9507-0.0750.1144-0.1718-0.32330.0518-0.26040.02490.08380.02320.282-0.01870.03680.03760.00520.055525.03334.08212.116
21.70430.7405-0.45383.1749-0.35771.27690.0267-0.1299-0.13460.2118-0.01690.18760.05560.0308-0.00980.28650.0173-0.020.01150.01160.036821.45832.33646.531
32.3791.5760.47573.04320.47071.1969-0.0274-0.0837-0.05340.13460.0589-0.29640.00540.0704-0.03150.31160.03630.04230.01960.00040.07765.558-9.40542.158
41.48631.0455-0.38334.1237-0.56121.3532-0.33220.29990.1056-0.85550.33770.21680.1409-0.1487-0.00550.645-0.19150.05080.1554-0.01520.07462.151-4.2798.165
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 337
2X-RAY DIFFRACTION2B8 - 337
3X-RAY DIFFRACTION3C8 - 339
4X-RAY DIFFRACTION4D8 - 337

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