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- PDB-4ffi: Crystal Structure of Levan Fructotransferase D54N mutant from Art... -

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Basic information

Entry
Database: PDB / ID: 4ffi
TitleCrystal Structure of Levan Fructotransferase D54N mutant from Arthrobacter ureafaciens in complex with levanbiose
ComponentsLevan fructotransferase
KeywordsTRANSFERASE / Glycoside Hydrolase
Function / homology
Function and homology information


sucrose alpha-glucosidase activity / sucrose catabolic process / transferase activity / cytoplasm
Similarity search - Function
Glycosyl hydrolase family 32, C-terminal / Glycosyl hydrolases family 32 C terminal / Glycoside hydrolase, family 32 / Glycosyl hydrolase family 32, N-terminal / Glycosyl hydrolases family 32 N-terminal domain / Glycosyl hydrolases family 32 / Exo-inulinase; domain 1 / Glycosyl hydrolase domain; family 43 / 5 Propeller / Tachylectin-2; Chain A ...Glycosyl hydrolase family 32, C-terminal / Glycosyl hydrolases family 32 C terminal / Glycoside hydrolase, family 32 / Glycosyl hydrolase family 32, N-terminal / Glycosyl hydrolases family 32 N-terminal domain / Glycosyl hydrolases family 32 / Exo-inulinase; domain 1 / 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
levanbiose / levantriose / Levan fructotransferase
Similarity search - Component
Biological speciesArthrobacter ureafaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Soaking Data / Resolution: 2.3 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 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / 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_molecule_features / pdbx_nonpoly_scheme / struct_conn / struct_ref_seq_dif / 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_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.src_method / _entity.type / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Feb 28, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)221,13714
Polymers217,5514
Non-polymers3,58510
Water15,259847
1
A: Levan fructotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,0723
Polymers54,3881
Non-polymers6852
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Levan fructotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,2353
Polymers54,3881
Non-polymers8472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Levan fructotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,4154
Polymers54,3881
Non-polymers1,0273
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Levan fructotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,4154
Polymers54,3881
Non-polymers1,0273
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)82.511, 168.125, 263.379
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: 54387.852 Da / Num. of mol.: 4 / Fragment: UNP residues 41-521 / Mutation: D54N
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: Polysaccharide
beta-D-fructofuranose-(2-6)-beta-D-fructofuranose / levanbiose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 342.297 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: levanbiose
DescriptorTypeProgram
DFrufb2-6DFrufb2-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[ha122h-2b_2-5]/1-1/a6-b2WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(6+2)][b-D-Fruf]{}}LINUCSPDB-CARE
#3: Polysaccharide beta-D-fructofuranose-(2-6)-beta-D-fructofuranose-(2-6)-beta-D-fructofuranose / levantriose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 504.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: levantriose
DescriptorTypeProgram
DFrufb2-6DFrufb2-6DFrufb2-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[ha122h-2b_2-5]/1-1-1/a6-b2_b6-c2WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(6+2)][b-D-Fruf]{[(6+2)][b-D-Fruf]{}}}LINUCSPDB-CARE
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 847 / 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: 4.2 Å3/Da / Density % sol: 70.7 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M MES pH6.5, 1M Lithium Sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 151733 / Num. obs: 145787

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: Soaking Data / Resolution: 2.3→50 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 5946
RfactorNum. reflection% reflection
Rfree0.2511 14570 8.9 %
Rwork0.2147 --
obs-145787 89.4 %
Solvent computationBsol: 28.8657 Å2
Displacement parametersBiso max: 64.1 Å2 / Biso mean: 22.6965 Å2 / Biso min: 4.69 Å2
Baniso -1Baniso -2Baniso -3
1--3.766 Å20 Å20 Å2
2--2.597 Å20 Å2
3---1.169 Å2
Refinement stepCycle: LAST / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14937 0 241 847 16025
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.1581.5
X-RAY DIFFRACTIONc_scbond_it1.8562
X-RAY DIFFRACTIONc_mcangle_it1.7552
X-RAY DIFFRACTIONc_scangle_it2.582.5
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
X-RAY DIFFRACTION6CBH_Stereo_20120501_2.par

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