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- PDB-1wmr: Crystal Structure of Isopullulanase from Aspergillus niger ATCC 9642 -

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Basic information

Entry
Database: PDB / ID: 1wmr
TitleCrystal Structure of Isopullulanase from Aspergillus niger ATCC 9642
ComponentsIsopullulanase
KeywordsHYDROLASE / pullulan / glycoside hydrolase family 49 / glycoprotein
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: 2.4 Å
AuthorsMizuno, M. / Tonozuka, T. / Miyasaka, Y. / Akeboshi, H. / Kamitori, S. / Nishikawa, A. / Sakano, Y.
CitationJournal: 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.
History
DepositionJul 15, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 19, 2005Provider: repository / Type: Initial release
Revision 1.1Jan 16, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Feb 7, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_validate_chiral / 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_atom_id / _atom_site.auth_comp_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_nonpoly_scheme.entity_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _struct_asym.entity_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 25, 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

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Assembly

Deposited unit
A: Isopullulanase
B: Isopullulanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,50222
Polymers120,0772
Non-polymers4,42420
Water10,755597
1
A: Isopullulanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,03010
Polymers60,0391
Non-polymers1,9919
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Isopullulanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,47212
Polymers60,0391
Non-polymers2,43311
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)99.512, 135.701, 83.804
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) / Production host: Pichia pastoris (fungus) / References: UniProt: O00105, isopullulanase
#2: 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.: 20
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
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 597 / 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: 2.4 Å3/Da / Density % sol: 47.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.4
Details: PEG8000, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-18B / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 4, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 45256 / Num. obs: 45256 / % possible obs: 99.9 % / Biso Wilson estimate: 20.8 Å2
Reflection shellResolution: 2.4→2.49 Å / % possible all: 99

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Processing

SoftwareName: CNS / Version: 1.1 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OGM

1ogm


Resolution: 2.4→49.76 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2580600.76 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.253 4553 10.1 %RANDOM
Rwork0.203 ---
all0.21 ---
obs0.203 45087 100 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 28.2284 Å2 / ksol: 0.357607 e/Å3
Displacement parametersBiso mean: 18.2 Å2
Baniso -1Baniso -2Baniso -3
1--1.35 Å20 Å20 Å2
2---1.86 Å20 Å2
3---3.21 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.27 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 2.4→49.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8484 0 280 597 9361
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.79
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.361.5
X-RAY DIFFRACTIONc_mcangle_it2.122
X-RAY DIFFRACTIONc_scbond_it1.82
X-RAY DIFFRACTIONc_scangle_it2.522.5
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.294 798 10.7 %
Rwork0.217 6627 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2CARBOHYDRATE.PARAMCARBOHYDRATE.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4WATER_REP.PARAMWATER_REP.TOP

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