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- PDB-1j0k: Crystal structure of neopullulanase E357Q complex with isopanose -

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Basic information

Entry
Database: PDB / ID: 1j0k
TitleCrystal structure of neopullulanase E357Q complex with isopanose
Componentsneopullulanase
KeywordsHYDROLASE / beta-alpha-barrels
Function / homology
Function and homology information


neopullulanase / neopullulanase activity / D-glucose binding / carbohydrate metabolic process / calcium ion binding / protein homodimerization activity / identical protein binding
Similarity search - Function
Glycoside hydrolase, family 13, N-terminal Ig-like domain / Alpha amylase, N-terminal ig-like domain / Maltogenic Amylase, C-terminal / Maltogenic Amylase, C-terminal domain / Oligo-1,6-glucosidase; domain 2 / Oligo-1,6-glucosidase; Domain 2 / Oligo-1,6-glucosidase, domain 2 / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain ...Glycoside hydrolase, family 13, N-terminal Ig-like domain / Alpha amylase, N-terminal ig-like domain / Maltogenic Amylase, C-terminal / Maltogenic Amylase, C-terminal domain / Oligo-1,6-glucosidase; domain 2 / Oligo-1,6-glucosidase; Domain 2 / 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 / Immunoglobulins / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like fold / Alpha-Beta Complex / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsHondoh, H. / Kuriki, T. / Matsuura, Y.
Citation
Journal: J.Mol.Biol. / Year: 2003
Title: Three-dimensional structure and substrate binding of Bacillus stearothermophilus neopullulanase
Authors: Hondoh, H. / Kuriki, T. / Matsuura, Y.
#1: Journal: J.Biol.Chem. / Year: 1992
Title: Action of neopullulanase. neopullulanase catalyzes both hydrolysis and transglycosylation at alpha-(1,4)- and alpha-(1,6)-glucosidic linkages
Authors: Takata, H. / Kuriki, T. / Okada, S. / Takesada, Y. / Iizuka, M. / Minamiura, N. / Imanaka, T.
#2: Journal: J.Bacteriol. / Year: 1989
Title: Pattern of action of Bacillus stearothermophilus neopullulanase on pullulan
Authors: Imanaka, T. / Kuriki, T.
#3: Journal: J.Bacteriol. / Year: 1988
Title: New type of pullulanase from Bacillus stearothermophilus and molecular cloning and expression of the gene in Bacillus subtilis
Authors: Kuriki, T. / Okada, S. / Imanaka, T.
History
DepositionNov 14, 2002Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 28, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / 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_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_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 10, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 2.2Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: neopullulanase
B: neopullulanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,2934
Polymers138,2842
Non-polymers1,0092
Water2,252125
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7680 Å2
ΔGint18 kcal/mol
Surface area42200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.006, 73.758, 123.246
Angle α, β, γ (deg.)90.00, 90.15, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is a dimer in the assymetric unit.

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Components

#1: Protein neopullulanase /


Mass: 69141.859 Da / Num. of mol.: 2 / Mutation: E357Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Plasmid: pUC129 / Production host: Escherichia coli (E. coli) / Strain (production host): TG-1 / References: UniProt: P38940, neopullulanase
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose


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


Mass: 18.015 Da / Num. of mol.: 125 / 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: 2.21 Å3/Da / Density % sol: 44.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 8000, sodium chloride, cacodylate , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
1100 mMsodium cacodylate1reservoirpH6.5
2180 mg/mlPEG80001reservoir
3300 mM1reservoirNaCl
45 mMsodium phosphate1droppH6.5
510 mM2-mercaptoethanol1drop
610 mg/mlenzyme1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL40B2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 2, 2001
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→20 Å / Num. obs: 20262 / % possible obs: 99.8 % / Observed criterion σ(F): 2
Reflection shellResolution: 3.2→3.4 Å / % possible all: 99.6
Reflection
*PLUS
Lowest resolution: 20 Å / Num. obs: 20308 / % possible obs: 99.6 % / Num. measured all: 75444 / Rmerge(I) obs: 0.11
Reflection shell
*PLUS
Highest resolution: 3.2 Å / Lowest resolution: 3.37 Å / % possible obs: 100 % / Rmerge(I) obs: 0.221

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
CNSrefinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→10 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.212 997 RANDOM
Rwork0.174 --
obs-19648 -
Refinement stepCycle: LAST / Resolution: 3.2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9778 0 68 125 9971
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
Refinement
*PLUS
Lowest resolution: 10 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS

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