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- PDB-2inu: Crystal structure of Inulin fructotransferase in the absence of s... -

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Basic information

Entry
Database: PDB / ID: 2inu
TitleCrystal structure of Inulin fructotransferase in the absence of substrate
ComponentsInulin fructotransferase
KeywordsLYASE / right-handed parallel beta-helix
Function / homology
Function and homology information


transferase activity
Similarity search - Function
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 / MAD / 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 1.3Oct 14, 2020Group: Database references / Derived calculations / Structure summary
Category: citation / entity ...citation / entity / struct / struct_conn / struct_site
Item: _citation.title / _entity.pdbx_description ..._citation.title / _entity.pdbx_description / _struct.pdbx_descriptor / _struct.title / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)130,9515
Polymers130,7913
Non-polymers1602
Water10,377576
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13490 Å2
ΔGint-60 kcal/mol
Surface area34010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)159.138, 91.907, 93.022
Angle α, β, γ (deg.)90.00, 124.75, 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 / Fragment: residues 41-450
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, EC: 4.2.2.18
#2: Chemical ChemComp-2PO / PHOSPHONATE


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


Mass: 18.015 Da / Num. of mol.: 576 / 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: 1.96 Å3/Da / Density % sol: 42.4 %
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: 0.97912, 0.97923, 0.97144
DetectorType: BRUKER PROTEUM 300 / Detector: CCD / Date: Oct 16, 2005
RadiationMonochromator: Double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979121
20.979231
30.971441
ReflectionResolution: 1.8→30 Å / Num. all: 101414 / Num. obs: 88334 / % possible obs: 87.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.4 % / Biso Wilson estimate: 14.3 Å2 / Rmerge(I) obs: 0.105 / Rsym value: 0.072 / Net I/σ(I): 19.8
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.483 / Mean I/σ(I) obs: 2.9 / Num. unique all: 10079 / Rsym value: 0.455 / % possible all: 99.9

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Processing

Software
NameClassification
HKL-2000data collection
SOLVEphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.8→30 Å / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.226 8377 -RANDOM
Rwork0.198 ---
all-101837 --
obs-83857 74.1 %-
Refinement stepCycle: LAST / Resolution: 1.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8946 0 8 576 9530
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_mcbond_it1.014
X-RAY DIFFRACTIONc_mcangle_it1.511
X-RAY DIFFRACTIONc_scbond_it1.769
X-RAY DIFFRACTIONc_scangle_it2.485

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