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- PDB-4fff: Crystal Structure of Levan Fructotransferase from Arthrobacter ur... -

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Basic information

Entry
Database: PDB / ID: 4fff
TitleCrystal Structure of Levan Fructotransferase from Arthrobacter ureafaciens
ComponentsLevan fructotransferase
KeywordsHYDROLASE / glycoside hydrolase
Function / homology
Function and homology information


hydrolase activity, hydrolyzing O-glycosyl compounds / transferase activity / carbohydrate metabolic process
Similarity search - Function
Glycosyl hydrolase family 32, C-terminal / Glycosyl hydrolases family 32 C terminal / Exo-inulinase; domain 1 / Glycoside hydrolase, family 32 / Glycosyl hydrolase family 32, N-terminal / Glycosyl hydrolases family 32 N-terminal domain / Glycosyl hydrolases family 32 / Glycosyl hydrolase domain; family 43 / 5 Propeller / Tachylectin-2; Chain A ...Glycosyl hydrolase family 32, C-terminal / Glycosyl hydrolases family 32 C terminal / Exo-inulinase; domain 1 / Glycoside hydrolase, family 32 / Glycosyl hydrolase family 32, N-terminal / Glycosyl hydrolases family 32 N-terminal domain / Glycosyl hydrolases family 32 / Glycosyl hydrolase domain; family 43 / 5 Propeller / Tachylectin-2; Chain A / Glycosyl hydrolase, five-bladed beta-propellor domain superfamily / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Levan fructotransferase
Similarity search - Component
Biological speciesArthrobacter ureafaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.57 Å
AuthorsPark, J. / Rhee, S.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Structural and functional basis for substrate specificity and catalysis of levan fructotransferase.
Authors: Park, J. / Kim, M.I. / Park, Y.D. / Shin, I. / Cha, J. / Kim, C.H. / Rhee, S.
History
DepositionJun 1, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 18, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 29, 2012Group: Database references
Revision 1.2Sep 26, 2012Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Levan fructotransferase
B: Levan fructotransferase
C: Levan fructotransferase
D: Levan fructotransferase


Theoretical massNumber of molelcules
Total (without water)216,0584
Polymers216,0584
Non-polymers00
Water12,773709
1
A: Levan fructotransferase


Theoretical massNumber of molelcules
Total (without water)54,0141
Polymers54,0141
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Levan fructotransferase


Theoretical massNumber of molelcules
Total (without water)54,0141
Polymers54,0141
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Levan fructotransferase


Theoretical massNumber of molelcules
Total (without water)54,0141
Polymers54,0141
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Levan fructotransferase


Theoretical massNumber of molelcules
Total (without water)54,0141
Polymers54,0141
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)81.958, 166.625, 261.964
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Levan fructotransferase


Mass: 54014.406 Da / Num. of mol.: 4 / Fragment: UNP residues 41-521
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arthrobacter ureafaciens (bacteria) / Gene: lftA / Production host: Escherichia coli (E. coli) / References: UniProt: Q9KJD0, EC: 4.2.2.16
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 709 / 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: 4.14 Å3/Da / Density % sol: 70.29 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1M Bis-Tris pH5.5, 1% PEG3350, 1M Ammonium sulfate, 3% 2-propanol, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 6C1 / Wavelength: 0.97949,0.97961,0.97181
DetectorType: ADSC QUANTUM 210 / Detector: CCD
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979491
20.979611
30.971811
ReflectionResolution: 2.57→50 Å / Num. all: 112528 / Num. obs: 104570

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.57→50 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 7958
RfactorNum. reflection% reflection
Rfree0.2556 10489 9.1 %
Rwork0.212 --
obs-104570 91 %
Solvent computationBsol: 26.966 Å2
Displacement parametersBiso max: 63.12 Å2 / Biso mean: 25.9512 Å2 / Biso min: 1 Å2
Baniso -1Baniso -2Baniso -3
1--10.104 Å20 Å20 Å2
2--16.817 Å20 Å2
3----6.713 Å2
Refinement stepCycle: LAST / Resolution: 2.57→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14936 0 0 709 15645
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.1021.5
X-RAY DIFFRACTIONc_scbond_it1.8182
X-RAY DIFFRACTIONc_mcangle_it1.7752
X-RAY DIFFRACTIONc_scangle_it2.6372.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.param
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION4CNS_TOPPAR:ion.param
X-RAY DIFFRACTION5CNS_TOPPAR:carbohydrate.param

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