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- PDB-2inv: Crystal structure of Inulin fructotransferase in the presence of ... -

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Basic information

Entry
Database: PDB / ID: 2inv
TitleCrystal structure of Inulin fructotransferase in the presence of di-fructose
ComponentsInulin fructotransferase
KeywordsLYASE / right-handed parallel beta-helix / protein-carbohydrate complex
Function / homology
Function and homology information


Inulin fructotransferase, beta helix repeat / Beta helix repeat of Inulin fructotransferase / Periplasmic copper-binding protein (NosD) / Single-stranded right-handed beta-helix, Pectin lyase-like / Pectate Lyase C-like / Pectin lyase fold / Pectin lyase fold/virulence factor / 3 Solenoid / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Mainly Beta
Similarity search - Domain/homology
PHOSPHONATE / Inulin fructotransferase
Similarity search - Component
Biological speciesBacillus sp. snu-7 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsRhee, S. / Jung, W.S.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Structural and functional insights into intramolecular fructosyl transfer by inulin fructotransferase
Authors: Jung, W.S. / Hong, C.K. / Lee, S. / Kim, C.S. / Kim, S.J. / Kim, S.I. / Rhee, S.
History
DepositionOct 9, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 26, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
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 / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_atom_id_2 / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 14, 2020Group: Database references / Structure summary
Category: chem_comp / citation ...chem_comp / citation / entity / struct
Item: _chem_comp.pdbx_synonyms / _citation.title ..._chem_comp.pdbx_synonyms / _citation.title / _entity.pdbx_description / _struct.pdbx_descriptor / _struct.title
Revision 2.2Oct 25, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 2.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Inulin fructotransferase
B: Inulin fructotransferase
C: Inulin fructotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,9778
Polymers130,7913
Non-polymers1,1875
Water11,259625
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16180 Å2
ΔGint-35 kcal/mol
Surface area32960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)159.166, 91.900, 92.916
Angle α, β, γ (deg.)90.00, 124.82, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Inulin fructotransferase


Mass: 43596.852 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus sp. snu-7 (bacteria) / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3)pLysS
References: UniProt: Q3SAG3, inulin fructotransferase (DFA-III-forming)
#2: Polysaccharide beta-D-fructofuranose-(2-1)-beta-D-fructofuranose


Type: oligosaccharide / Mass: 342.297 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DFrufb2-1DFrufb2-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[ha122h-2b_2-5]/1-1/a1-b2WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{}LINUCSPDB-CARE
#3: Chemical ChemComp-2PO / PHOSPHONATE


Mass: 79.980 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: HO3P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 625 / Source method: isolated from a natural source / Formula: H2O
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: 1.95 Å3/Da / Density % sol: 42.29 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 1.0M ammonium phosphate, 0.1M imidazole, 0.2M sodium chloride, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 6B / Wavelength: 1.12714 Å
DetectorType: BRUKER PROTEUM 300 / Detector: CCD / Date: Oct 16, 2005
RadiationMonochromator: Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12714 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 101292 / Num. obs: 93099 / % possible obs: 91.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7 % / Biso Wilson estimate: 15.7 Å2 / Rmerge(I) obs: 0.07 / Rsym value: 0.058 / Net I/σ(I): 29.6
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.286 / Mean I/σ(I) obs: 5 / Num. unique all: 10070 / Rsym value: 0.27 / % possible all: 100

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Processing

Software
NameClassification
HKL-2000data collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2INU

2inu


Resolution: 1.8→50 Å / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.227 9334 -RANDOM
Rwork0.207 ---
all-101649 --
obs-93055 82.4 %-
Refinement stepCycle: LAST / Resolution: 1.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8946 0 77 625 9648
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_mcbond_it0.782
X-RAY DIFFRACTIONc_mcangle_it1.189
X-RAY DIFFRACTIONc_scbond_it1.234
X-RAY DIFFRACTIONc_scangle_it1.651

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