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- PDB-2z8g: Aspergillus niger ATCC9642 isopullulanase complexed with isopanose -

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Basic information

Entry
Database: PDB / ID: 2z8g
TitleAspergillus niger ATCC9642 isopullulanase complexed with isopanose
ComponentsIsopullulanase
KeywordsHYDROLASE / isopullulanase / GH49 / dextranase / pullulan / beta-helix / Glycoprotein / Glycosidase / Secreted
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
Biological speciesAspergillus niger (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsMizuno, M. / Koide, A. / Yamamura, A. / Akeboshi, H. / Yoshida, H. / Kamitori, S. / Sakano, Y. / Nishikawa, A. / Tonozuka, T.
Citation
Journal: J.Mol.Biol. / Year: 2008
Title: Crystal Structure of Aspergillus niger Isopullulanase, a Member of Glycoside Hydrolase Family 49
Authors: Mizuno, M. / Koide, A. / Yamamura, A. / Akeboshi, H. / Yoshida, H. / Kamitori, S. / Sakano, Y. / Nishikawa, A. / Tonozuka, T.
#1: Journal: Eur.J.Biochem. / Year: 2004
Title: Insights into the reaction mechanism of glycosyl hydrolase family 49: Site-directed mutagenesis and substrate preference of isopullulanase
Authors: Akeboshi, H. / Tonozuka, T. / Furukawa, T. / Ichikawa, K. / Aoki, H. / Shimonishi, A. / Nishikawa, A. / Sakano, Y.
#2: Journal: Biosci.Biotechnol.Biochem. / Year: 2003
Title: Construction of an efficient expression system for Aspergillus isopullulanase in Pichia pastoris, and a simple purification method
Authors: Akeboshi, H. / Kashiwagi, Y. / Aoki, H. / Tonozuka, T. / Nishikawa, A. / Sakano, Y.
History
DepositionSep 5, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 18, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / 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_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.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Apr 3, 2024Group: 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

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Assembly

Deposited unit
A: Isopullulanase
B: Isopullulanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,17427
Polymers120,0772
Non-polymers6,09725
Water20,9511163
1
A: Isopullulanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,19814
Polymers60,0391
Non-polymers3,15913
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Isopullulanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,97613
Polymers60,0391
Non-polymers2,93812
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)83.672, 99.387, 134.987
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Isopullulanase /


Mass: 60038.719 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus niger (mold) / Strain: ATCC9642 / Plasmid: pHIL-S1 / Production host: Pichia pastoris (fungus) / Strain (production host): GS115 / References: UniProt: O00105, isopullulanase
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-6)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 504.438 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-6DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5][a2122h-1a_1-5]/1-2-2/a6-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(6+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}}LINUCSPDB-CARE
#3: 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.: 23
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
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1163 / 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: 2.34 Å3/Da / Density % sol: 47.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 8.75% PEG 8000, 100mM sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 24, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 123214 / Num. obs: 123214 / % possible obs: 99.3 % / Redundancy: 10.4 % / Biso Wilson estimate: 18.5 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 33.9
Reflection shellResolution: 1.7→1.76 Å / Rmerge(I) obs: 0.375 / Mean I/σ(I) obs: 3 / Num. unique all: 11669 / % possible all: 95.1

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Processing

Software
NameVersionClassification
CNS1.1refinement
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: a predicted model generated using the Swiss-model server, Akeboshi et al., Eur. J. Biochem., 271, 4420-4427, 2004

Resolution: 1.7→49.69 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 2743571.38 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.211 12328 10 %RANDOM
Rwork0.187 ---
obs0.187 123129 99.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 45.9137 Å2 / ksol: 0.347184 e/Å3
Displacement parametersBiso mean: 21.1 Å2
Baniso -1Baniso -2Baniso -3
1--0.31 Å20 Å20 Å2
2---0.98 Å20 Å2
3---1.29 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.13 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 1.7→49.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8484 0 390 1163 10037
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d26.4
X-RAY DIFFRACTIONc_improper_angle_d0.75
X-RAY DIFFRACTIONc_mcbond_it1.11.5
X-RAY DIFFRACTIONc_mcangle_it1.662
X-RAY DIFFRACTIONc_scbond_it1.722
X-RAY DIFFRACTIONc_scangle_it2.452.5
LS refinement shellResolution: 1.7→1.81 Å / Rfactor Rfree error: 0.006 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.272 2018 10.2 %
Rwork0.246 17736 -
obs--96.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2carbohydrate.paramcarbohydrate.top
X-RAY DIFFRACTION3water_rep.paramwater.top

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