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

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Basic information

Entry
Database: PDB / ID: 3roj
TitleD-fructose 1,6-bisphosphatase class 2/sedoheptulose 1,7-bisphosphatase of Synechocystis sp. PCC 6803
ComponentsD-fructose 1,6-bisphosphatase class 2/sedoheptulose 1,7-bisphosphatase
KeywordsHYDROLASE / fructose-1 / 6-/sedoheptulose-1 / 7-bisphosphatase
Function / homology
Function and homology information


sedoheptulose-bisphosphatase activity / sedoheptulose-bisphosphatase / glycerol metabolic process / fructose-bisphosphatase / reductive pentose-phosphate cycle / 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 / D-fructose 1,6-bisphosphatase class 2/sedoheptulose 1,7-bisphosphatase
Similarity search - Component
Biological speciesSynechocystis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 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 1.1Nov 1, 2023Group: 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_ref_seq_dif / struct_site
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_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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.3Oct 16, 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)166,73757
Polymers162,6134
Non-polymers4,12453
Water15,871881
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12130 Å2
ΔGint-29 kcal/mol
Surface area49160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)144.282, 144.282, 168.795
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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Protein , 1 types, 4 molecules ABCD

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


Mass: 40653.344 Da / Num. of mol.: 4
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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Non-polymers , 6 types, 934 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-AMP / ADENOSINE MONOPHOSPHATE


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


Mass: 96.063 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: SO4
#5: Chemical...
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 881 / 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: 3.12 Å3/Da / Density % sol: 60.56 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100mM HEPES, 1.6M Ammonium Sulfate, 7-9% glycerol, 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 12, 2010
RadiationMonochromator: multilayer optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→25.95 Å / Num. all: 87598 / Num. obs: 87598 / % possible obs: 99.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 14.7 % / Biso Wilson estimate: 34.9 Å2 / Rmerge(I) obs: 0.119 / Net I/σ(I): 19.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allDiffraction-ID% possible all
2.3-2.426.60.5512.912260195.4
7.27-25.9516.30.031542793197.6

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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: 3D1R

3d1r


Resolution: 2.3→25.542 Å / Occupancy max: 1 / Occupancy min: 0.38 / FOM work R set: 0.8723 / SU ML: 0.27 / σ(F): 1.34 / Phase error: 20.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2044 4396 5.02 %RANDOM
Rwork0.1835 ---
all0.1845 87525 --
obs0.1845 87525 99.3 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.13 Å2 / ksol: 0.384 e/Å3
Displacement parametersBiso max: 115.81 Å2 / Biso mean: 30.8998 Å2 / Biso min: 0 Å2
Baniso -1Baniso -2Baniso -3
1-3.1167 Å20 Å2-0 Å2
2--3.1167 Å20 Å2
3----6.2334 Å2
Refinement stepCycle: LAST / Resolution: 2.3→25.542 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10242 0 214 881 11337
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00310638
X-RAY DIFFRACTIONf_angle_d0.81614416
X-RAY DIFFRACTIONf_chiral_restr0.0481648
X-RAY DIFFRACTIONf_plane_restr0.0021888
X-RAY DIFFRACTIONf_dihedral_angle_d13.7573921
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3-2.32610.28311380.29092599273792
2.3261-2.35350.28021260.28452593271994
2.3535-2.38210.29091510.2612667281896
2.3821-2.41230.3011570.26152744290198
2.4123-2.4440.26581440.24152744288899
2.444-2.47750.25331700.230227592929100
2.4775-2.51280.22821480.214627692917100
2.5128-2.55030.23741340.216127892923100
2.5503-2.59010.22891540.215327802934100
2.5901-2.63250.23111390.210927882927100
2.6325-2.67790.24351310.205228202951100
2.6779-2.72650.22051430.201127702913100
2.7265-2.77890.20781760.202327712947100
2.7789-2.83550.24931270.194927862913100
2.8355-2.89710.20741510.186827952946100
2.8971-2.96440.21971230.186328112934100
2.9644-3.03840.221500.186927732923100
3.0384-3.12040.19571850.181327652950100
3.1204-3.21210.24561370.183628062943100
3.2121-3.31560.19691460.174227792925100
3.3156-3.43380.20161400.176527892929100
3.4338-3.57090.18541430.164727962939100
3.5709-3.7330.17831450.153827842929100
3.733-3.92910.14971470.145427952942100
3.9291-4.17430.16691620.139427972959100
4.1743-4.4950.16651460.13527892935100
4.495-4.94440.15721520.144628122964100
4.9444-5.65310.19971470.181128022949100
5.6531-7.09690.22151440.219728052949100
7.0969-25.54360.18851400.183128522992100

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