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

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Basic information

Entry
Database: PDB / ID: 5oey
TitleCrystal structure of Leishmania major fructose-1,6-bisphosphatase in holo 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 / cytosol / cytoplasm
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
CITRIC ACID / : / : / PHOSPHATE ION / fructose-bisphosphatase
Similarity search - Component
Biological speciesLeishmania major (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry / _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)156,85022
Polymers155,4904
Non-polymers1,36018
Water2,540141
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17440 Å2
ΔGint-121 kcal/mol
Surface area42790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.010, 104.150, 137.740
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: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRASPASPAA8 - 3368 - 336
21THRTHRASPASPBB8 - 3368 - 336
12THRTHRASPASPAA8 - 3368 - 336
22THRTHRASPASPCC8 - 3368 - 336
13THRTHRASPASPAA8 - 3368 - 336
23THRTHRASPASPDD8 - 3368 - 336
14THRTHRARGARGBB8 - 3378 - 337
24THRTHRARGARGCC8 - 3378 - 337
15THRTHRARGARGBB8 - 3378 - 337
25THRTHRARGARGDD8 - 3378 - 337
16PROPROARGARGCC7 - 3377 - 337
26PROPROARGARGDD7 - 3377 - 337

NCS ensembles :
ID
1
2
3
4
5
6

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
FBP protein / fructose-1 / 6-bisphosphatase


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

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Non-polymers , 5 types, 159 molecules

#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mn
#4: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / 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: 2.12 Å3/Da / Density % sol: 42.04 %
Crystal growTemperature: 290.15 K / Method: vapor diffusion, hanging drop / pH: 6
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: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Aug 1, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.8→55.14 Å / Num. obs: 33215 / % possible obs: 100 % / Redundancy: 13.7 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 12.3
Reflection shellResolution: 2.8→2.9 Å / Rmerge(I) obs: 0.74 / Mean I/σ(I) obs: 3.9 / Num. unique obs: 3280 / % possible all: 100

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Processing

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

5fbp


Resolution: 2.8→55.14 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.878 / SU B: 14.842 / SU ML: 0.285 / Cross valid method: THROUGHOUT / ESU R Free: 0.39 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24125 1677 5 %RANDOM
Rwork0.19306 ---
obs0.19549 31538 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 33.427 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å2-0 Å2-0 Å2
2---2.16 Å20 Å2
3---2.11 Å2
Refinement stepCycle: 1 / Resolution: 2.8→55.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9913 0 58 141 10112
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01910159
X-RAY DIFFRACTIONr_bond_other_d0.0080.029728
X-RAY DIFFRACTIONr_angle_refined_deg1.651.96313729
X-RAY DIFFRACTIONr_angle_other_deg1.703322352
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.28251262
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.90823.395433
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.93151765
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4841571
X-RAY DIFFRACTIONr_chiral_restr0.0870.21520
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211402
X-RAY DIFFRACTIONr_gen_planes_other0.0060.022329
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_it2.4973.1915075
X-RAY DIFFRACTIONr_mcbond_other2.4933.195074
X-RAY DIFFRACTIONr_mcangle_it4.2784.7686325
X-RAY DIFFRACTIONr_mcangle_other4.2784.7686326
X-RAY DIFFRACTIONr_scbond_it2.5733.4985084
X-RAY DIFFRACTIONr_scbond_other2.5723.4975082
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.3425.1167403
X-RAY DIFFRACTIONr_long_range_B_refined9.45629.05442969
X-RAY DIFFRACTIONr_long_range_B_other9.45629.05342968
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)
11A376280.12
12B376280.12
21A388460.1
22C388460.1
31A352440.11
32D352440.11
41B379760.11
42C379760.11
51B355540.11
52D355540.11
61C358160.11
62D358160.11
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 111 -
Rwork0.271 2316 -
obs--100 %

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