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

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Basic information

Entry
Database: PDB / ID: 5ofu
TitleCrystal structure of Leishmania major fructose-1,6-bisphosphatase in T-state.
ComponentsFBP protein
KeywordsTRANSFERASE / 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
ADENOSINE MONOPHOSPHATE / 6-O-phosphono-beta-D-fructofuranose / fructose-bisphosphatase
Similarity search - Component
Biological speciesLeishmania major (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.62 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 11, 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 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,99014
Polymers155,4904
Non-polymers2,50010
Water2,054114
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20440 Å2
ΔGint-136 kcal/mol
Surface area43220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.590, 109.250, 140.510
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: PRO / Beg label comp-ID: PRO / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASNASNAA7 - 3387 - 338
21ASNASNBB7 - 3387 - 338
12ARGARGAA7 - 3377 - 337
22ARGARGCC7 - 3377 - 337
13ASNASNAA7 - 3387 - 338
23ASNASNDD7 - 3387 - 338
14ARGARGBB7 - 3377 - 337
24ARGARGCC7 - 3377 - 337
15ASNASNBB7 - 3387 - 338
25ASNASNDD7 - 3387 - 338
16ARGARGCC7 - 3377 - 337
26ARGARGDD7 - 3377 - 337

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: Chemical
ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#3: Sugar
ChemComp-F6P / 6-O-phosphono-beta-D-fructofuranose / FRUCTOSE-6-PHOSPHATE / 6-O-phosphono-beta-D-fructose / 6-O-phosphono-D-fructose / 6-O-phosphono-fructose


Type: D-saccharide, beta linking / Mass: 260.136 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C6H13O9P
IdentifierTypeProgram
b-D-Fruf6PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / 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: 2.24 Å3/Da / Density % sol: 44.99 %
Crystal growTemperature: 290.15 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 19% w/v PEG 3,350, 5% glycerol, 79% well buffer (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: I03 / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 1, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.62→70.25 Å / Num. obs: 42513 / % possible obs: 99.9 % / Redundancy: 5.5 % / Net I/σ(I): 12.4
Reflection shellResolution: 2.62→2.714 Å / Rmerge(I) obs: 0.77

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Processing

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

5fbp


Resolution: 2.62→70.25 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.947 / SU B: 25.146 / SU ML: 0.245 / Cross valid method: THROUGHOUT / ESU R Free: 0.291 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21634 2147 5.1 %RANDOM
Rwork0.18874 ---
obs0.19015 40367 99.75 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å
Displacement parametersBiso mean: 56.203 Å2
Baniso -1Baniso -2Baniso -3
1--2.87 Å2-0 Å2-0 Å2
2--1.06 Å2-0 Å2
3---1.81 Å2
Refinement stepCycle: 1 / Resolution: 2.62→70.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10007 0 158 114 10279
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01910374
X-RAY DIFFRACTIONr_bond_other_d0.0050.029877
X-RAY DIFFRACTIONr_angle_refined_deg1.4161.97814049
X-RAY DIFFRACTIONr_angle_other_deg1.278322717
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.14951273
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.05823.379435
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.12151781
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6741572
X-RAY DIFFRACTIONr_chiral_restr0.0750.21564
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02111525
X-RAY DIFFRACTIONr_gen_planes_other0.0030.022367
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_it2.6033.3265119
X-RAY DIFFRACTIONr_mcbond_other2.5953.3265118
X-RAY DIFFRACTIONr_mcangle_it4.2054.9766383
X-RAY DIFFRACTIONr_mcangle_other4.2064.9776384
X-RAY DIFFRACTIONr_scbond_it3.2713.7555255
X-RAY DIFFRACTIONr_scbond_other3.273.7555255
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.2455.4717667
X-RAY DIFFRACTIONr_long_range_B_refined7.63226.63811333
X-RAY DIFFRACTIONr_long_range_B_other7.63426.62511324
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)
11A393900.05
12B393900.05
21A387480.07
22C387480.07
31A388700.07
32D388700.07
41B386420.06
42C386420.06
51B389840.07
52D389840.07
61C381480.08
62D381480.08
LS refinement shellResolution: 2.62→2.688 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 167 -
Rwork0.297 2916 -
obs--99.55 %
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)
10.322-0.05-0.02040.15360.12580.8272-0.0576-0.051-0.0340.03330.02590.0530.04970.07520.03180.55850.02030.03160.0281-0.00230.0327-24.835-24.05917.272
20.2948-0.05370.26990.4716-0.09380.512-0.04890.1216-0.0045-0.04420.0460.04990.03230.03270.00290.5527-0.03510.0070.0836-0.00280.0145-33.051-16.953-13.434
30.2978-0.1407-0.38040.10450.27750.83880.05790.02320.0573-0.05290.0172-0.0162-0.13630.0624-0.07510.6349-0.04160.02910.02740.00440.0245-23.72625.63-3.806
40.5196-0.25510.0150.5056-0.42340.5649-0.1138-0.1993-0.07830.05760.15930.0356-0.1455-0.0477-0.04550.63070.02770.03050.09450.01660.0344-34.11719.27126.653
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 338
2X-RAY DIFFRACTION2B7 - 338
3X-RAY DIFFRACTION3C7 - 337
4X-RAY DIFFRACTION4D7 - 338

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