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- PDB-3ldk: Crystal Structure of A. japonicus CB05 -

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Basic information

Entry
Database: PDB / ID: 3ldk
TitleCrystal Structure of A. japonicus CB05
ComponentsFructosyltransferase
KeywordsHYDROLASE / Five-bladed beta-propeller fold
Function / homology
Function and homology information


hydrolase activity, hydrolyzing O-glycosyl compounds / 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 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
sucrose / Beta-fructofuranosidase
Similarity search - Component
Biological speciesAspergillus japonicus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsChuankhayan, P. / Chen, C.J. / Chaing, C.M. / Hsieh, C.Y. / Chen, C.D. / Hsieh, Y.C.
CitationJournal: To be Published
Title: Crystal structure of Aspergillus japonicus fructosyltransferase complex with donor/acceptor substrates reveal complete sbusites in the active site for catalysis
Authors: Chuankhayan, P. / Hsieh, C.Y. / Huang, Y.C. / Hsieh, Y.Y. / Guan, H.H. / Hsieh, Y.C. / Tien, Y.C. / Chen, C.D. / Chaing, C.M. / Chen, C.J.
History
DepositionJan 13, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / 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_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.type / _entity.formula_weight / _entity.pdbx_description / _entity.type
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Mar 20, 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

Downloads & links

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Assembly

Deposited unit
A: Fructosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,2852
Polymers68,9431
Non-polymers3421
Water4,107228
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Fructosyltransferase
hetero molecules

A: Fructosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,5704
Polymers137,8852
Non-polymers6852
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,-y,z1
Buried area1860 Å2
ΔGint-9 kcal/mol
Surface area46200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.350, 110.967, 66.129
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Fructosyltransferase


Mass: 68942.562 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus japonicus (mold) / Production host: Escherichia coli (E. coli) / References: UniProt: Q1W3Z7*PLUS
#2: Polysaccharide beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose / sucrose /


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: sucrose
DescriptorTypeProgram
DFrufb2-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[ha122h-2b_2-5][a2122h-1a_1-5]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(2+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 228 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsA SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST. THE AUTHOR HAS ALREADY ...A SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST. THE AUTHOR HAS ALREADY DEPOSITED THE DNA SEQUENCE OF THIS PROTEIN IN GENBANK DATABASES, THE ACCESSION NUMBER IS GU356596.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.64 Å3/Da / Density % sol: 53.47 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 8% PEG, 0.1M Sodium acetate, 150mM LiCl, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11101
21101
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSRRC BL13B111
SYNCHROTRONSPring-8 BL12B221
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDDec 30, 2008
ADSC QUANTUM 4r2CCDDec 21, 2008
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si 111 CHANNELSINGLE WAVELENGTHMx-ray1
2Si 111 CHANNELSINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. all: 36134 / Num. obs: 36134 / % possible obs: 95.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Rmerge(I) obs: 0.053 / Rsym value: 0.053 / Net I/σ(I): 30.3
Reflection shellHighest resolution: 2.2 Å / % possible all: 98.1

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→30 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.264 3336 -RANDOM
Rwork0.224 ---
all0.229 37838 --
obs0.229 33506 88.6 %-
Refinement stepCycle: LAST / Resolution: 2.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4883 0 23 228 5134

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