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- PDB-5a5l: Structure of dual function FBPase SBPase from Thermosynechococcus... -

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Basic information

Entry
Database: PDB / ID: 5a5l
TitleStructure of dual function FBPase SBPase from Thermosynechococcus elongatus
ComponentsD-FRUCTOSE 1,6-BISPHOSPHATASE CLASS 2/SEDOHEPTULOSE 1,7-BISPHOSPHATASE
KeywordsHYDROLASE / CALVIN CYCLE / CYANOBACTERIA / PHOSPHATASE
Function / homology
Function and homology information


sedoheptulose-bisphosphatase / sedoheptulose-bisphosphatase activity / glycerol metabolic process / reductive pentose-phosphate cycle / fructose-bisphosphatase / fructose 1,6-bisphosphate 1-phosphatase activity / gluconeogenesis / metal ion binding
Similarity search - Function
D-Maltodextrin-Binding Protein; domain 2 - #90 / Fructose-1,6-bisphosphatase class 2/Sedoheputulose-1,7-bisphosphatase / Bacterial fructose-1,6-bisphosphatase, glpX-encoded / 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
PHOSPHATE ION / 7-O-phosphono-alpha-L-galacto-hept-2-ulopyranose / D-fructose 1,6-bisphosphatase class 2/sedoheptulose 1,7-bisphosphatase
Similarity search - Component
Biological speciesTHERMOSYNECHOCOCCUS ELONGATUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.34 Å
AuthorsCotton, C.A.R. / Kabasakal, B. / Miah, N. / Murray, J.W.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2015
Title: Structure of the Dual-Function Fructose-1,6/Sedoheptulose-1, 7-Bisphosphatase from Thermosynechococcus Elongatus Bound with Sedoheptulose-7-Phosphate.
Authors: Cotton, C.A.R. / Kabasakal, B. / Miah, N. / Murray, J.W.
History
DepositionJun 19, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 14, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2015Group: Database references
Revision 2.0Nov 21, 2018Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _struct_conn.ptnr1_label_atom_id
Revision 2.1Jul 29, 2020Group: Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_database_status / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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_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_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_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.2Jan 10, 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
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: D-FRUCTOSE 1,6-BISPHOSPHATASE CLASS 2/SEDOHEPTULOSE 1,7-BISPHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9206
Polymers39,4621
Non-polymers4585
Water1,33374
1
A: D-FRUCTOSE 1,6-BISPHOSPHATASE CLASS 2/SEDOHEPTULOSE 1,7-BISPHOSPHATASE
hetero molecules

A: D-FRUCTOSE 1,6-BISPHOSPHATASE CLASS 2/SEDOHEPTULOSE 1,7-BISPHOSPHATASE
hetero molecules

A: D-FRUCTOSE 1,6-BISPHOSPHATASE CLASS 2/SEDOHEPTULOSE 1,7-BISPHOSPHATASE
hetero molecules

A: D-FRUCTOSE 1,6-BISPHOSPHATASE CLASS 2/SEDOHEPTULOSE 1,7-BISPHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,68124
Polymers157,8494
Non-polymers1,83220
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_555-x,-y,z1
crystal symmetry operation8_556-y,-x,-z+11
crystal symmetry operation15_556y,x,-z+11
Buried area11250 Å2
ΔGint-138.8 kcal/mol
Surface area49170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)143.090, 143.090, 76.430
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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Components

#1: Protein D-FRUCTOSE 1,6-BISPHOSPHATASE CLASS 2/SEDOHEPTULOSE 1,7-BISPHOSPHATASE / FBPASE CLASS 2/SBPASE / DUAL FUNCTION SBPASE FBPASE


Mass: 39462.195 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMOSYNECHOCOCCUS ELONGATUS (bacteria)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): KRX
References: UniProt: Q8DJE9, sedoheptulose-bisphosphatase, fructose-bisphosphatase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Sugar ChemComp-VTB / 7-O-phosphono-alpha-L-galacto-hept-2-ulopyranose / [(2~{S},3~{S},4~{R},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5,6-tetrakis(oxidanyl)oxan-2-yl]methyl dihydrogen phosphate / 7-O-phosphono-alpha-L-galacto-hept-2-ulose / 7-O-phosphono-L-galacto-hept-2-ulose / 7-O-phosphono-galacto-hept-2-ulose


Type: L-saccharide, alpha linking / Mass: 290.162 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H15O10P
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / 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: 2.61 Å3/Da / Density % sol: 53 % / Description: NONE
Crystal growDetails: 0.06 M NAHEPES (PH 7.5), 0.12 M MGCL2, 27% V/V PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9173
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 3, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9173 Å / Relative weight: 1
ReflectionResolution: 2.34→67.42 Å / Num. obs: 17040 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 8.51 % / Biso Wilson estimate: 51.33 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 9.96
Reflection shellResolution: 2.34→2.4 Å / Redundancy: 8.52 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 1.23 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2R8T

2r8t


Resolution: 2.34→67.416 Å / SU ML: 0.28 / σ(F): 0 / Phase error: 23.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2243 862 5.1 %
Rwork0.1657 --
obs0.1685 17028 99.88 %
Refinement stepCycle: LAST / Resolution: 2.34→67.416 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2537 0 26 74 2637
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072595
X-RAY DIFFRACTIONf_angle_d1.0543504
X-RAY DIFFRACTIONf_dihedral_angle_d13.875973
X-RAY DIFFRACTIONf_chiral_restr0.045398
X-RAY DIFFRACTIONf_plane_restr0.004460
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.34-2.48670.28951510.20622645X-RAY DIFFRACTION100
2.4867-2.67870.26651400.19452633X-RAY DIFFRACTION100
2.6787-2.94820.26341530.19272676X-RAY DIFFRACTION100
2.9482-3.37480.28271410.18562677X-RAY DIFFRACTION100
3.3748-4.25180.17711440.1592702X-RAY DIFFRACTION100
4.2518-67.44360.21131330.14712833X-RAY DIFFRACTION99
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)
14.02360.01692.32623.787-0.67934.03390.111-0.1175-0.32380.2142-0.06050.00530.0869-0.0892-0.03840.3764-0.01350.04180.2549-0.01060.4183-6.043-25.850442.6187
22.43461.20051.51683.76432.63926.7753-0.2028-0.2864-1.71860.4720.31140.2470.84980.6185-0.24410.610.02170.05280.4494-0.01120.7614-4.5795-38.786134.2187
35.4641-5.3721.7335.3176-1.25926.03770.3046-0.1413-1.3898-0.2128-0.17410.82951.143-0.4271-0.19920.7017-0.08070.07260.3409-0.03230.5697-9.4383-37.540438.2171
41.2237-2.64542.31136.4097-6.77618.8999-0.3889-0.5309-2.88481.31630.0679-1.29950.1656-0.54110.48510.7131-0.20880.14860.9140.28371.8061-25.6342-37.804940.1721
57.04434.53285.03854.73491.54365.2499-0.214-0.1073-0.1894-0.25640.17380.1262-0.029-0.05220.02750.33590.03660.02740.3105-0.09310.4569-4.9334-27.590233.8416
64.25850.87480.28922.3481-0.41272.5142-0.21870.57860.0586-0.48510.0684-0.116-0.02720.3980.1580.4367-0.08740.02310.4851-0.05250.319710.9351-20.815621.1933
76.395-0.17525.10195.058-1.11344.20880.02330.5364-1.06630.38140.06-0.3351.01140.17-0.0841.00750.03570.25740.6501-0.23250.839913.5451-43.805224.5136
85.5768-0.9616-2.30944.07481.53387.2978-0.16271.3711-0.7778-0.8016-0.18240.19730.01910.16480.31990.5735-0.1357-0.06510.6211-0.1970.5751-1.0762-33.35917.0107
99.16273.12046.53827.33371.36074.785-0.49830.62290.4333-0.02450.3366-0.0915-0.76930.45020.33230.3563-0.06240.0010.4105-0.02690.43910.3168-15.832737.4137
108.41730.89484.72462.8789-1.14739.01250.16770.00450.24780.17470.0762-0.1289-0.36810.4217-0.31120.27890.01330.03310.2362-0.02630.4235-7.346-13.441740.8952
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 0:49)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 50:62)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 63:76)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 77:83)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 84:125)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 126:253)
7X-RAY DIFFRACTION7(CHAIN A AND RESID 254:269)
8X-RAY DIFFRACTION8(CHAIN A AND RESID 270:290)
9X-RAY DIFFRACTION9(CHAIN A AND RESID 291:308)
10X-RAY DIFFRACTION10(CHAIN A AND RESID 309:337)

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