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- PDB-1j0h: Crystal structure of Bacillus stearothermophilus neopullulanase -

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Basic information

Entry
Database: PDB / ID: 1j0h
TitleCrystal structure of Bacillus stearothermophilus neopullulanase
Componentsneopullulanase
KeywordsHYDROLASE / beta-alpha-barrels
Function / homology
Function and homology information


neopullulanase activity / neopullulanase / 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 / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like fold / Immunoglobulins / 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: 1.9 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 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_label_seq_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_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)138,4015
Polymers138,2862
Non-polymers1163
Water28,8421601
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5710 Å2
ΔGint-40 kcal/mol
Surface area42920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.713, 72.762, 123.640
Angle α, β, γ (deg.)90.00, 90.84, 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: 69142.844 Da / Num. of mol.: 2
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: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1601 / 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: 1.94 Å3/Da / Density % sol: 36.08 %
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, 1999
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→32 Å / Num. obs: 90768 / % possible obs: 94.2 % / Observed criterion σ(F): 2
Reflection shellResolution: 1.9→2.02 Å / % possible all: 71.9
Reflection
*PLUS
Num. obs: 90890 / Num. measured all: 321350 / Rmerge(I) obs: 0.059
Reflection shell
*PLUS
Lowest resolution: 2 Å / % possible obs: 71.1 % / Rmerge(I) obs: 0.187

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
CNS1.1refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→10 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.203 4517 5 %RANDOM
Rwork0.163 ---
obs-90106 --
Refinement stepCycle: LAST / Resolution: 1.9→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9778 0 3 1601 11382
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
Software
*PLUS
Classification: refinement
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 10 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

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