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- PDB-3wwg: Crystal structure of the N-glycan-deficient variant N448A of isop... -

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Basic information

Entry
Database: PDB / ID: 3wwg
TitleCrystal structure of the N-glycan-deficient variant N448A of isopullulanase complexed with isopanose
ComponentsIsopullulanase
KeywordsHYDROLASE / beta-helix / glycoside hydrolase family 49
Function / homology
Function and homology information


isopullulanase / isopullulanase activity / metabolic process / extracellular region
Similarity search - Function
Dex49a from penicillium minioluteum complex, domain 1 / Dextranase, N-terminal / Glycoside hydrolase, family 49, C-terminal / Glycoside hydrolase, family 49, N-terminal domain / Dextranase, N-terminal / Isopullulanase beta-solenoid repeat / Dextranase, beta solenoid repeat / Glycosyl hydrolase family 49 / Glycosyl hydrolase family 49 N-terminal Ig-like domain / Isopullulanase beta-solenoid repeat ...Dex49a from penicillium minioluteum complex, domain 1 / Dextranase, N-terminal / Glycoside hydrolase, family 49, C-terminal / Glycoside hydrolase, family 49, N-terminal domain / Dextranase, N-terminal / Isopullulanase beta-solenoid repeat / Dextranase, beta solenoid repeat / Glycosyl hydrolase family 49 / Glycosyl hydrolase family 49 N-terminal Ig-like domain / Isopullulanase beta-solenoid repeat / Beta solenoid repeat from Dextranase / Single-stranded right-handed beta-helix, Pectin lyase-like / Pectate Lyase C-like / Pectin lyase fold / Pectin lyase fold/virulence factor / 3 Solenoid / Sandwich / Mainly Beta
Similarity search - Domain/homology
alpha-maltose / Isopullulanase
Similarity search - Component
Biological speciesAspergillus niger (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsMiyazaki, T. / Yashiro, H. / Nishikawa, A. / Tonozuka, T.
CitationJournal: J.Biochem. / Year: 2015
Title: The side chain of a glycosylated asparagine residue is important for the stability of isopullulanase
Authors: Miyazaki, T. / Yashiro, H. / Nishikawa, A. / Tonozuka, T.
History
DepositionJun 17, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 12, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 15, 2015Group: 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 / pdbx_struct_assembly_gen / struct_asym / 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_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_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 / _pdbx_struct_assembly_gen.asym_id_list / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 8, 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: Isopullulanase
B: Isopullulanase
C: Isopullulanase
D: Isopullulanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)247,74638
Polymers239,9834
Non-polymers7,76334
Water11,223623
1
A: Isopullulanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,7659
Polymers59,9961
Non-polymers1,7708
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Isopullulanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,8869
Polymers59,9961
Non-polymers1,8918
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Isopullulanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,32911
Polymers59,9961
Non-polymers2,33310
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Isopullulanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,7659
Polymers59,9961
Non-polymers1,7708
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)96.400, 108.100, 116.000
Angle α, β, γ (deg.)90.00, 103.90, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Isopullulanase /


Mass: 59995.695 Da / Num. of mol.: 4 / Fragment: UNP residues 20-564 / Mutation: N448A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus niger (mold) / Strain: ATCC 9642 / Gene: ipuA / Plasmid: pHIL-S1 / Production host: Pichia pastoris (fungus) / Strain (production host): GS115 / References: UniProt: O00105, isopullulanase
#2: Polysaccharide alpha-D-glucopyranose-(1-6)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpa1-6DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5][a2122h-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(6+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#4: Sugar...
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 32
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 623 / 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: 2.44 Å3/Da / Density % sol: 49.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.7
Details: 10% PEG8000, 50mM sodium acetate buffer, pH 4.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 2, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 114159 / % possible obs: 97.4 % / Rmerge(I) obs: 0.071
Reflection shellResolution: 2.2→2.32 Å / Rmerge(I) obs: 0.334 / Mean I/σ(I) obs: 3.6 / % possible all: 92.4

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.7.0029refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1X0C

1x0c


Resolution: 2.2→34.04 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.926 / Cross valid method: THROUGHOUT / ESU R: 0.286 / ESU R Free: 0.205 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22366 5738 5 %RANDOM
Rwork0.18254 ---
obs0.18458 108391 97.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 29.857 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å2-0 Å20 Å2
2---0 Å2-0 Å2
3----0 Å2
Refinement stepCycle: LAST / Resolution: 2.2→34.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16694 0 494 623 17811
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0217675
X-RAY DIFFRACTIONr_bond_other_d00.0215603
X-RAY DIFFRACTIONr_angle_refined_deg1.2211.95524207
X-RAY DIFFRACTIONr_angle_other_deg3.735335679
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.48152147
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.68624.774817
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.182152434
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5781564
X-RAY DIFFRACTIONr_chiral_restr0.0680.22722
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02120406
X-RAY DIFFRACTIONr_gen_planes_other0.0050.024218
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 443 -
Rwork0.246 7456 -
obs--91.84 %

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