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- PDB-3ueq: Crystal structure of amylosucrase from Neisseria polysaccharea in... -

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Basic information

Entry
Database: PDB / ID: 3ueq
TitleCrystal structure of amylosucrase from Neisseria polysaccharea in complex with turanose
ComponentsAmylosucrase
KeywordsTRANSFERASE / beta/alpha-barrel / glycoside hydrolase / amylose synthesis / sucrose isomerization / glucosyltransferase / carbohydrate
Function / homology
Function and homology information


amylosucrase / amylosucrase activity / carbohydrate metabolic process / extracellular region
Similarity search - Function
Amylosucrase, catalytic domain / RNA polymerase sigma factor, region 2, helix turn helix motif / Oligo-1,6-glucosidase; domain 2 / Oligo-1,6-glucosidase; Domain 2 / Rna Polymerase Sigma Factor; Chain: A / Oligo-1,6-glucosidase, domain 2 / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Golgi alpha-mannosidase II ...Amylosucrase, catalytic domain / RNA polymerase sigma factor, region 2, helix turn helix motif / Oligo-1,6-glucosidase; domain 2 / Oligo-1,6-glucosidase; Domain 2 / Rna Polymerase Sigma Factor; Chain: A / Oligo-1,6-glucosidase, domain 2 / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha-Beta Complex / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
beta-turanose / 3-O-alpha-D-glucopyranosyl-D-fructose / DI(HYDROXYETHYL)ETHER / Amylosucrase
Similarity search - Component
Biological speciesNeisseria polysaccharea (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsGuerin, F. / Pizzut-Serin, S. / Potocki-Veronese, G. / Guillet, V. / Mourey, L. / Remaud-Simeon, M. / Andre, I. / Tranier, S.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Structural Investigation of the Thermostability and Product Specificity of Amylosucrase from the Bacterium Deinococcus geothermalis.
Authors: Guerin, F. / Barbe, S. / Pizzut-Serin, S. / Potocki-Veronese, G. / Guieysse, D. / Guillet, V. / Monsan, P. / Mourey, L. / Remaud-Simeon, M. / Andre, I. / Tranier, S.
History
DepositionOct 31, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 14, 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.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 2.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Amylosucrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,6794
Polymers71,8881
Non-polymers7913
Water13,818767
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)96.030, 116.270, 60.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-999-

HOH

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Components

#1: Protein Amylosucrase


Mass: 71888.453 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria polysaccharea (bacteria) / Strain: ATCC 43768 / Gene: ams / Plasmid: pGEX-6P3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9ZEU2, amylosucrase
#2: Polysaccharide alpha-D-glucopyranose-(1-3)-beta-D-fructofuranose / beta-turanose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-turanose
DescriptorTypeProgram
DGlcpa1-3DFrufb2-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[ha122h-2b_2-5][a2122h-1a_1-5]/1-2/a3-b1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(3+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Sugar ChemComp-OTU / 3-O-alpha-D-glucopyranosyl-D-fructose / 3-O-alpha-D-glucosyl-D-fructose / 3-O-D-glucosyl-D-fructose / 3-O-glucosyl-D-fructose


Type: D-saccharide / Mass: 342.296 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H22O11
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 767 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsG537D MUTATION IS A PCR ARTIFACT

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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: 2.35 Å3/Da / Density % sol: 47.64 %
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 30% PEG 6000, 0.1 M HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 285.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 6, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 1.85→29.27 Å / Num. all: 58575 / Num. obs: 55312 / % possible obs: 99.47 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.85→1.95 Å

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Processing

Software
NameVersionClassification
DNAdata collection
PHASERphasing
REFMAC5.5.0072refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1G5A

1g5a


Resolution: 1.85→29.07 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.938 / SU B: 2.438 / SU ML: 0.073 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18564 2953 5.1 %RANDOM
Rwork0.14713 ---
obs0.14911 58309 99.47 %-
all-58575 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.555 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å2-0 Å2-0 Å2
2---0.23 Å2-0 Å2
3---0.35 Å2
Refinement stepCycle: LAST / Resolution: 1.85→29.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5016 0 53 767 5836
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0225240
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7571.9447137
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2815633
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.9823.911271
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.26515799
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7441536
X-RAY DIFFRACTIONr_chiral_restr0.1330.2762
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0214112
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0211.53152
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.64325068
X-RAY DIFFRACTIONr_scbond_it2.77632088
X-RAY DIFFRACTIONr_scangle_it4.1674.52067
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 207 -
Rwork0.206 4054 -
obs--99.98 %

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