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- PDB-3rpl: D-fructose 1,6-bisphosphatase class 2/sedoheptulose 1,7-bisphosph... -

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Basic information

Entry
Database: PDB / ID: 3rpl
TitleD-fructose 1,6-bisphosphatase class 2/sedoheptulose 1,7-bisphosphatase of Synechocystis sp. PCC 6803 in complex with FRUCTOSE-1,6-BISPHOSPHATE
Components(D-fructose 1,6-bisphosphatase class 2/sedoheptulose 1,7- ...) x 2
KeywordsHYDROLASE / fructose-1 / 6-/sedoheptulose-1 / 7-bisphosphatase
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 / fructose 1,6-bisphosphate metabolic process / 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
ADENOSINE MONOPHOSPHATE / 1,6-di-O-phosphono-beta-D-fructofuranose / D-fructose 1,6-bisphosphatase class 2/sedoheptulose 1,7-bisphosphatase
Similarity search - Component
Biological speciesSynechocystis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsHu, X. / Hui, D. / Lingling, F. / Jian, W.
CitationJournal: To be Published
Title: New insights into the structural and interactional basis for a promising route towards fructose-1,6-/sedoheptulose-1,7-bisphosphatases controlling
Authors: Hu, X. / Lingling, F.
History
DepositionApr 26, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 2, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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 / _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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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.pdbx_leaving_atom_flag / _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_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Nov 1, 2023Group: 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
Revision 1.3Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
B: D-fructose 1,6-bisphosphatase class 2/sedoheptulose 1,7-bisphosphatase
C: D-fructose 1,6-bisphosphatase class 2/sedoheptulose 1,7-bisphosphatase
D: D-fructose 1,6-bisphosphatase class 2/sedoheptulose 1,7-bisphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,98442
Polymers162,5814
Non-polymers4,40338
Water13,872770
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11840 Å2
ΔGint-30 kcal/mol
Surface area49300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.222, 145.222, 169.104
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

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D-fructose 1,6-bisphosphatase class 2/sedoheptulose 1,7- ... , 2 types, 4 molecules ACDB

#1: Protein D-fructose 1,6-bisphosphatase class 2/sedoheptulose 1,7-bisphosphatase / FBPase class 2/SBPase


Mass: 40637.344 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis (bacteria) / Strain: PCC 6803 / Gene: slr2094 / Plasmid: pET28a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)
References: UniProt: P73922, fructose-bisphosphatase, sedoheptulose-bisphosphatase
#2: Protein D-fructose 1,6-bisphosphatase class 2/sedoheptulose 1,7-bisphosphatase / FBPase class 2/SBPase


Mass: 40669.344 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis (bacteria) / Strain: PCC 6803 / Gene: slr2094 / Plasmid: pET28a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)
References: UniProt: P73922, fructose-bisphosphatase, sedoheptulose-bisphosphatase

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Sugars , 1 types, 4 molecules

#4: Sugar
ChemComp-FBP / 1,6-di-O-phosphono-beta-D-fructofuranose / BETA-FRUCTOSE-1,6-DIPHOSPHATE / FRUCTOSE-1,6-BISPHOSPHATE / 1,6-di-O-phosphono-beta-D-fructose / 1,6-di-O-phosphono-D-fructose / 1,6-di-O-phosphono-fructose


Type: D-saccharide, beta linking / Mass: 340.116 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C6H14O12P2
IdentifierTypeProgram
b-D-Fruf1PO36PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 6 types, 804 molecules

#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#6: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#7: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#8: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 770 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 3.17 Å3/Da / Density % sol: 61.15 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100mM HEPES, 1.6M Ammonium Sulfate, 7-9% glycerol, 10mM FBP, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SEALED TUBE / Type: OXFORD DIFFRACTION ENHANCE ULTRA / Wavelength: 1.5418 Å
DetectorType: OXFORD ONYX CCD / Detector: CCD / Date: Aug 14, 2010 / Details: multilayer optics
RadiationMonochromator: multilayer optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→25.72 Å / Num. all: 78184 / Num. obs: 78184 / % possible obs: 99.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.4 % / Biso Wilson estimate: 35.2 Å2 / Rmerge(I) obs: 0.131 / Net I/σ(I): 12.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allDiffraction-ID% possible all
2.4-2.533.90.6092.210899195.1
7.59-25.726.50.02835.42495197.4

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Processing

Software
NameVersionClassification
CrysalisProdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.7_650)refinement
CrysalisProdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ROJ

3roj


Resolution: 2.4→25.719 Å / Occupancy max: 1 / Occupancy min: 0.4 / FOM work R set: 0.88 / SU ML: 0.33 / σ(F): 1.34 / Phase error: 19.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2066 3937 5.04 %RANDOM
Rwork0.1662 ---
all0.1683 78126 --
obs0.1683 78126 99.22 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 31.799 Å2 / ksol: 0.372 e/Å3
Displacement parametersBiso max: 100.54 Å2 / Biso mean: 27.4848 Å2 / Biso min: 8.96 Å2
Baniso -1Baniso -2Baniso -3
1-3.6144 Å2-0 Å2-0 Å2
2--3.6144 Å20 Å2
3----7.2288 Å2
Refinement stepCycle: LAST / Resolution: 2.4→25.719 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10204 0 251 770 11225
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01110618
X-RAY DIFFRACTIONf_angle_d1.18814402
X-RAY DIFFRACTIONf_chiral_restr0.0681655
X-RAY DIFFRACTIONf_plane_restr0.0041871
X-RAY DIFFRACTIONf_dihedral_angle_d14.9383901
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 28

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4-2.42930.29181310.25132456258793
2.4293-2.460.30091430.23442514265794
2.46-2.49230.27611160.22932558267496
2.4923-2.52640.27951240.22252615273997
2.5264-2.56250.27581500.21972621277198
2.5625-2.60070.26891250.210226562781100
2.6007-2.64130.27121440.203526722816100
2.6413-2.68460.22251420.192326832825100
2.6846-2.73080.24441380.190826412779100
2.7308-2.78040.22241520.184326572809100
2.7804-2.83380.2421450.175526432788100
2.8338-2.89160.19681370.1726822819100
2.8916-2.95440.22781270.168926542781100
2.9544-3.0230.23171390.172327002839100
3.023-3.09850.20431420.171226742816100
3.0985-3.18210.20931430.17326582801100
3.1821-3.27560.1931360.164526472783100
3.2756-3.38110.19951680.163126792847100
3.3811-3.50160.21871180.158626742792100
3.5016-3.64150.18911610.146226462807100
3.6415-3.80670.1871720.144526302802100
3.8067-4.00670.16461450.133626772822100
4.0067-4.25670.17321260.127526972823100
4.2567-4.58360.1551660.117426562822100
4.5836-5.04180.18571430.132626872830100
5.0418-5.76410.20591380.167826772815100
5.7641-7.23530.21571230.197127252848100
7.2353-25.72040.17281430.167127102853100

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